/static/formatHelp.html

https://bitbucket.org/cistrome/cistrome-harvard/ · HTML · 665 lines · 596 code · 36 blank · 33 comment · 0 complexity · 474f0d9804a2769354e4cc782047766b MD5 · raw file 

    

  1. <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
    2. 

  2. 	"http://www.w3.org/TR/html4/loose.dtd">
    3. 

  3. <html>
    4. 

  4. <head>
    5. 

  5. <title>Galaxy Data Formats</title>
    6. 

  6. <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
    7. 

  7. <meta http-equiv="Content-Style-Type" content="text/css">
    8. 

  8. <style type="text/css">
    9. 

  9. 	hr  { margin-top: 3ex; margin-bottom: 1ex; border: 1px inset }
    10. 

  10. </style>
    11. 

  11. </head>
    12. 

  12. <body>
    13. 

  13. <h2>Galaxy Data Formats</h2>
    14. 

  14. <p>
    15. 

  15. <br>
    16. 

  16. 

  17. <h3>Dataset missing?</h3>
    18. 

  18. <p>
    19. 

  19. If you have a dataset in your history that is not appearing in the
    20. 

  20. drop-down selector for a tool, the most common reason is that it has
    21. 

  21. the wrong format.  Each Galaxy dataset has an associated file format
    22. 

  22. recorded in its metadata, and tools will only list datasets from your
    23. 

  23. history that have a format compatible with that particular tool.  Of
    24. 

  24. course some of these datasets might not actually contain relevant
    25. 

  25. data, or even the correct columns needed by the tool, but filtering
    26. 

  26. by format at least makes the list to select from a bit shorter.
    27. 

  27. <p>
    28. 

  28. Some of the formats are defined hierarchically, going from very
    29. 

  29. general ones like <a href="#tab">Tabular</a> (which includes any text
    30. 

  30. file with tab-separated columns), to more restrictive sub-formats
    31. 

  31. like <a href="#interval">Interval</a> (where three of the columns
    32. 

  32. must be the chromosome, start position, and end position), and on
    33. 

  33. to even more specific ones such as <a href="#bed">BED</a> that have
    34. 

  34. additional requirements.  So for example if a tool's required input
    35. 

  35. format is Tabular, then all of your history items whose format is
    36. 

  36. recorded as Tabular will be listed, along with those in all
    37. 

  37. sub-formats that also qualify as Tabular (Interval, BED, GFF, etc.).
    38. 

  38. <p>
    39. 

  39. There are two usual methods for changing a dataset's format in
    40. 

  40. Galaxy: if the file contents are already in the required format but
    41. 

  41. the metadata is wrong (perhaps because the Auto-detect feature of the
    42. 

  42. Upload File tool guessed it incorrectly), you can fix the metadata
    43. 

  43. manually by clicking on the pencil icon beside that dataset in your
    44. 

  44. history.  Or, if the file contents really are in a different format,
    45. 

  45. Galaxy provides a number of format conversion tools (e.g. in the
    46. 

  46. Text Manipulation and Convert Formats categories).  For instance,
    47. 

  47. if the tool you want to run requires Tabular but your columns are
    48. 

  48. delimited by spaces or commas, you can use the "Convert delimiters
    49. 

  49. to TAB" tool under Text Manipulation to reformat your data.  However
    50. 

  50. if your files are in a completely unsupported format, then you need
    51. 

  51. to convert them yourself before uploading.
    52. 

  52. <p>
    53. 

  53. <hr>
    54. 

  54. 

  55. <h3>Format Descriptions</h3>
    56. 

  56. <ul>
    57. 

  57. <li><a href="#ab1">AB1</a>
    58. 

  58. <li><a href="#axt">AXT</a>
    59. 

  59. <li><a href="#bam">BAM</a>
    60. 

  60. <li><a href="#bed">BED</a>
    61. 

  61. <li><a href="#bedgraph">BedGraph</a>
    62. 

  62. <li><a href="#binseq">Binseq.zip</a>
    63. 

  63. <li><a href="#fasta">FASTA</a>
    64. 

  64. <li><a href="#fastqsolexa">FastqSolexa</a>
    65. 

  65. <li><a href="#fped">FPED</a>
    66. 

  66. <li><a href="#gd_indivs">gd_indivs</a>
    67. 

  67. <li><a href="#gd_ped">gd_ped</a>
    68. 

  68. <li><a href="#gd_sap">gd_sap</a>
    69. 

  69. <li><a href="#gd_snp">gd_snp</a>
    70. 

  70. <li><a href="#gff">GFF</a>
    71. 

  71. <li><a href="#gff3">GFF3</a>
    72. 

  72. <li><a href="#gtf">GTF</a>
    73. 

  73. <li><a href="#html">HTML</a>
    74. 

  74. <li><a href="#interval">Interval</a>
    75. 

  75. <li><a href="#lav">LAV</a>
    76. 

  76. <li><a href="#lped">LPED</a>
    77. 

  77. <li><a href="#maf">MAF</a>
    78. 

  78. <li><a href="#mastervar">MasterVar</a>
    79. 

  79. <li><a href="#pbed">PBED</a>
    80. 

  80. <li><a href="#pgSnp">pgSnp</a>
    81. 

  81. <li><a href="#psl">PSL</a>
    82. 

  82. <li><a href="#scf">SCF</a>
    83. 

  83. <li><a href="#sff">SFF</a>
    84. 

  84. <li><a href="#table">Table</a>
    85. 

  85. <li><a href="#tab">Tabular</a>
    86. 

  86. <li><a href="#txtseqzip">Txtseq.zip</a>
    87. 

  87. <li><a href="#vcf">VCF</a>
    88. 

  88. <li><a href="#wig">Wiggle custom track</a>
    89. 

  89. <li><a href="#text">Other text type</a>
    90. 

  90. </ul>
    91. 

  91. <p>
    92. 

  92. 

  93. <div><a name="ab1"></a></div>
    94. 

  94. <hr>
    95. 

  95. <strong>AB1</strong>
    96. 

  96. <p>
    97. 

  97. This is one of the ABIF family of binary sequence formats from
    98. 

  98. Applied Biosystems Inc.
    99. 

  99. <!-- Their PDF
    100. 

  100. <a href="http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf"
    101. 

  101. >format specification</a> is unfortunately password-protected. -->
    102. 

  102. Files should have a '<code>.ab1</code>' file extension.  You must
    103. 

  103. manually select this file format when uploading the file.
    104. 

  104. <p>
    105. 

  105. 

  106. <div><a name="axt"></a></div>
    107. 

  107. <hr>
    108. 

  108. <strong>AXT</strong>
    109. 

  109. <p>
    110. 

  110. Used for pairwise alignment output from BLASTZ, after post-processing.
    111. 

  111. Each alignment block contains three lines: a summary line and two
    112. 

  112. sequence lines.  Blocks are separated from one another by blank lines.
    113. 

  113. The summary line contains chromosomal position and size information
    114. 

  114. about the alignment, and consists of nine required fields.
    115. 

  115. <a href="http://main.genome-browser.bx.psu.edu/goldenPath/help/axt.html"
    116. 

  116. >More information</a>
    117. 

  117. <!-- (not available on Main)
    118. 

  118. <dl><dt>Can be converted to:
    119. 

  119. <dd><ul>
    120. 

  120. <li>FASTA<br>
    121. 

  121. Convert Formats &rarr; AXT to FASTA
    122. 

  122. <li>LAV<br>
    123. 

  123. Convert Formats &rarr; AXT to LAV
    124. 

  124. </ul></dl>
    125. 

  125. -->
    126. 

  126. <p>
    127. 

  127. 

  128. <div><a name="bam"></a></div>
    129. 

  129. <hr>
    130. 

  130. <strong>BAM</strong>
    131. 

  131. <p>
    132. 

  132. A binary alignment file compressed in the BGZF format with a
    133. 

  133. '<code>.bam</code>' file extension.
    134. 

  134. <!-- You must manually select this file format when uploading the file. -->
    135. 

  135. <a href="http://samtools.sourceforge.net/SAM1.pdf">SAM</a>
    136. 

  136. is the human-readable text version of this format.
    137. 

  137. <dl><dt>Can be converted to:
    138. 

  138. <dd><ul>
    139. 

  139. <li>SAM<br>
    140. 

  140. NGS: SAM Tools &rarr; BAM-to-SAM
    141. 

  141. <li>Pileup<br>
    142. 

  142. NGS: SAM Tools &rarr; Generate pileup
    143. 

  143. <li>Interval<br>
    144. 

  144. First convert to Pileup as above, then use
    145. 

  145. NGS: SAM Tools &rarr; Pileup-to-Interval
    146. 

  146. </ul></dl>
    147. 

  147. <p>
    148. 

  148. 

  149. <div><a name="bed"></a></div>
    150. 

  150. <hr>
    151. 

  151. <strong>BED</strong>
    152. 

  152. <p>
    153. 

  153. <ul>
    154. 

  154. <li> also qualifies as Tabular
    155. 

  155. <li> also qualifies as Interval
    156. 

  156. </ul>
    157. 

  157. This tab-separated format describes a genomic interval, but has
    158. 

  158. strict field specifications for use in genome browsers.  BED files
    159. 

  159. can have from 3 to 12 columns, but the order of the columns matters,
    160. 

  160. and only the end ones can be omitted.  Some groups of columns must
    161. 

  161. be all present or all absent.  As in Interval format (but unlike
    162. 

  162. GFF and its relatives), the interval endpoints use a 0-based,
    163. 

  163. half-open numbering system.
    164. 

  164. <a href="http://main.genome-browser.bx.psu.edu/goldenPath/help/hgTracksHelp.html#BED"
    165. 

  165. >Field specifications</a>
    166. 

  166. <p>
    167. 

  167. Example:
    168. 

  168. <pre>
    169. 

  169. chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
    170. 

  170. chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
    171. 

  171. </pre>
    172. 

  172. <dl><dt>Can be converted to:
    173. 

  173. <dd><ul>
    174. 

  174. <li>GFF<br>
    175. 

  175. Convert Formats &rarr; BED-to-GFF
    176. 

  176. </ul></dl>
    177. 

  177. <p>
    178. 

  178. 

  179. <div><a name="bedgraph"></a></div>
    180. 

  180. <hr>
    181. 

  181. <strong>BedGraph</strong>
    182. 

  182. <p>
    183. 

  183. <ul>
    184. 

  184. <li> also qualifies as Tabular
    185. 

  185. <li> also qualifies as Interval
    186. 

  186. <li> also qualifies as BED
    187. 

  187. </ul>
    188. 

  188. <a href="http://main.genome-browser.bx.psu.edu/goldenPath/help/bedgraph.html"
    189. 

  189. >BedGraph</a> is a BED file with the name column being a float value
    190. 

  190. that is displayed as a wiggle score in tracks.  Unlike in Wiggle
    191. 

  191. format, the exact value of this score can be retrieved after being
    192. 

  192. loaded as a track.
    193. 

  193. <p>
    194. 

  194. 

  195. <div><a name="binseq"></a></div>
    196. 

  196. <hr>
    197. 

  197. <strong>Binseq.zip</strong>
    198. 

  198. <p>
    199. 

  199. A zipped archive consisting of binary sequence files in either AB1
    200. 

  200. or SCF format.  All files in this archive must have the same file
    201. 

  201. extension which is one of '<code>.ab1</code>' or '<code>.scf</code>'.
    202. 

  202. You must manually select this file format when uploading the file.
    203. 

  203. <p>
    204. 

  204. 

  205. <div><a name="fasta"></a></div>
    206. 

  206. <hr>
    207. 

  207. <strong>FASTA</strong>
    208. 

  208. <p>
    209. 

  209. A sequence in 
    210. 

  210. <a href="http://www.ncbi.nlm.nih.gov/blast/fasta.shtml">FASTA</a>
    211. 

  211. format consists of a single-line description, followed by lines of
    212. 

  212. sequence data.  The first character of the description line is a
    213. 

  213. greater-than ('<code>&gt;</code>') symbol.  All lines should be
    214. 

  214. shorter than 80 characters.
    215. 

  215. <pre>
    216. 

  216. >sequence1
    217. 

  217. atgcgtttgcgtgc
    218. 

  218. gtcggtttcgttgc
    219. 

  219. >sequence2
    220. 

  220. tttcgtgcgtatag
    221. 

  221. tggcgcggtga
    222. 

  222. </pre>
    223. 

  223. <dl><dt>Can be converted to:
    224. 

  224. <dd><ul>
    225. 

  225. <li>Tabular<br>
    226. 

  226. Convert Formats &rarr; FASTA-to-Tabular
    227. 

  227. </ul></dl>
    228. 

  228. <p>
    229. 

  229. 

  230. <div><a name="fastqsolexa"></a></div>
    231. 

  231. <hr>
    232. 

  232. <strong>FastqSolexa</strong>
    233. 

  233. <p>
    234. 

  234. <a href="http://maq.sourceforge.net/fastq.shtml">FastqSolexa</a>
    235. 

  235. is the Illumina (Solexa) variant of the FASTQ format, which stores
    236. 

  236. sequences and quality scores in a single file.
    237. 

  237. <pre>
    238. 

  238. @seq1  
    239. 

  239. GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT  
    240. 

  240. +seq1  
    241. 

  241. hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh  
    242. 

  242. @seq2  
    243. 

  243. GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG  
    244. 

  244. +seq2  
    245. 

  245. hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
    246. 

  246. </pre>
    247. 

  247. Or 
    248. 

  248. <pre>
    249. 

  249. @seq1
    250. 

  250. GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
    251. 

  251. +seq1
    252. 

  252. 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
    253. 

  253. @seq2
    254. 

  254. GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
    255. 

  255. +seq2
    256. 

  256. 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
    257. 

  257. </pre>
    258. 

  258. <dl><dt>Can be converted to:
    259. 

  259. <dd><ul>
    260. 

  260. <li>FASTA<br>
    261. 

  261. NGS: QC and manipulation &rarr; Generic FASTQ manipulation &rarr; FASTQ to FASTA
    262. 

  262. <li>Tabular<br>
    263. 

  263. NGS: QC and manipulation &rarr; Generic FASTQ manipulation &rarr; FASTQ to Tabular
    264. 

  264. </ul></dl>
    265. 

  265. <p>
    266. 

  266. 

  267. <div><a name="fped"></a></div>
    268. 

  268. <hr>
    269. 

  269. <strong>FPED</strong>
    270. 

  270. <p>
    271. 

  271. Also known as the FBAT format, for use with the
    272. 

  272. <a href="http://biosun1.harvard.edu/~fbat/fbat.htm">FBAT</a> program.
    273. 

  273. It consists of a pedigree file and a phenotype file.
    274. 

  274. <p>
    275. 

  275. 

  276. <div><a name="gd_indivs"></a></div>
    277. 

  277. <hr>
    278. 

  278. <strong>ind</strong>
    279. 

  279. <p>
    280. 

  280. This format is a tabular file with the first column being the column number
    281. 

  281. (1 based)
    282. 

  282. from the gd_snp file where the individual/group starts.  The second column is
    283. 

  283. the label from the metadata for the individual/group.  The third is an alias
    284. 

  284. or blank.
    285. 

  285. <p>
    286. 

  286. 

  287. <div><a name="gd_sap"></a></div>
    288. 

  288. <hr>
    289. 

  289. <strong>gd_sap</strong>
    290. 

  290. <p>
    291. 

  291. This is a tabular file describing single amino-acid polymorphisms (SAPs).
    292. 

  292. You must manually select this file format when uploading the file.
    293. 

  293. <!--
    294. 

  294. <a href="http://www.bx.psu.edu/miller_lab/docs/formats/gd_sap_format.html"
    295. 

  295. >Field specifications</a>
    296. 

  296. -->
    297. 

  297. <p>
    298. 

  298. 

  299. <div><a name="gd_snp"></a></div>
    300. 

  300. <hr>
    301. 

  301. <strong>gd_snp</strong>
    302. 

  302. <p>
    303. 

  303. This is a tabular file describing SNPs in individuals or populations.
    304. 

  304. It contains the zero-based position of the SNP but not the range
    305. 

  305. required by BED or interval so can not be used in Genomic Operations without
    306. 

  306. adding an column for the end position.
    307. 

  307. You must manually select this file format when uploading the file.
    308. 

  308. <a href="http://www.bx.psu.edu/miller_lab/docs/formats/gd_snp_format.html"
    309. 

  309. >Field specifications</a>
    310. 

  310. <p>
    311. 

  311. 

  312. <div><a name="gff"></a></div>
    313. 

  313. <hr>
    314. 

  314. <strong>GFF</strong>
    315. 

  315. <p>
    316. 

  316. <ul>
    317. 

  317. <li> also qualifies as Tabular
    318. 

  318. </ul>
    319. 

  319. GFF is a tab-separated format somewhat similar to BED, but it has
    320. 

  320. different columns and is more flexible.  There are
    321. 

  321. <a href="http://main.genome-browser.bx.psu.edu/FAQ/FAQformat#format3"
    322. 

  322. >nine required fields</a>.
    323. 

  323. Note that unlike Interval and BED, GFF and its relatives (GFF3, GTF)
    324. 

  324. use 1-based inclusive coordinates to specify genomic intervals.
    325. 

  325. <dl><dt>Can be converted to:
    326. 

  326. <dd><ul>
    327. 

  327. <li>BED<br>
    328. 

  328. Convert Formats &rarr; GFF-to-BED
    329. 

  329. </ul></dl>
    330. 

  330. <p>
    331. 

  331. 

  332. <div><a name="gff3"></a></div>
    333. 

  333. <hr>
    334. 

  334. <strong>GFF3</strong>
    335. 

  335. <p>
    336. 

  336. <ul>
    337. 

  337. <li> also qualifies as Tabular
    338. 

  338. </ul>
    339. 

  339. The <a href="http://www.sequenceontology.org/gff3.shtml">GFF3</a>
    340. 

  340. format addresses the most common extensions to GFF, while attempting
    341. 

  341. to preserve compatibility with previous formats.
    342. 

  342. Note that unlike Interval and BED, GFF and its relatives (GFF3, GTF)
    343. 

  343. use 1-based inclusive coordinates to specify genomic intervals.
    344. 

  344. <p>
    345. 

  345. 

  346. <div><a name="gtf"></a></div>
    347. 

  347. <hr>
    348. 

  348. <strong>GTF</strong>
    349. 

  349. <p>
    350. 

  350. <ul>
    351. 

  351. <li> also qualifies as Tabular
    352. 

  352. </ul>
    353. 

  353. <a href="http://main.genome-browser.bx.psu.edu/FAQ/FAQformat#format4"
    354. 

  354. >GTF</a> is a format for describing genes and other features associated
    355. 

  355. with DNA, RNA, and protein sequences.  It is a refinement to GFF that
    356. 

  356. tightens the specification.
    357. 

  357. Note that unlike Interval and BED, GFF and its relatives (GFF3, GTF)
    358. 

  358. use 1-based inclusive coordinates to specify genomic intervals.
    359. 

  359. <!-- (not available on Main)
    360. 

  360. <dl><dt>Can be converted to:
    361. 

  361. <dd><ul>
    362. 

  362. <li>BedGraph<br>
    363. 

  363. Convert Formats &rarr; GTF-to-BEDGraph
    364. 

  364. </ul></dl>
    365. 

  365. -->
    366. 

  366. <p>
    367. 

  367. 

  368. <div><a name="html"></a></div>
    369. 

  369. <hr>
    370. 

  370. <strong>HTML</strong>
    371. 

  371. <p>
    372. 

  372. This format is an HTML web page.  Click the eye icon next to the
    373. 

  373. dataset to view it in your browser.
    374. 

  374. <p>
    375. 

  375. 

  376. <div><a name="interval"></a></div>
    377. 

  377. <hr>
    378. 

  378. <strong>Interval</strong>
    379. 

  379. <p>
    380. 

  380. <ul>
    381. 

  381. <li> also qualifies as Tabular
    382. 

  382. </ul>
    383. 

  383. This Galaxy format represents genomic intervals.  It is tab-separated,
    384. 

  384. but has the added requirement that three of the columns must be the
    385. 

  385. chromosome name, start position, and end position, where the positions
    386. 

  386. use a 0-based, half-open numbering system (see below).  An optional
    387. 

  387. strand column can also be specified, and an initial header row can
    388. 

  388. be used to label the columns, which do not have to be in any special
    389. 

  389. order.  Arbitrary additional columns can also be present.
    390. 

  390. <p>
    391. 

  391. Required fields:
    392. 

  392. <ul>
    393. 

  393. <li>CHROM - The name of the chromosome (e.g. chr3, chrY, chr2_random)
    394. 

  394.     or contig (e.g. ctgY1).
    395. 

  395. <li>START - The starting position of the feature in the chromosome or
    396. 

  396.     contig.  The first base in a chromosome is numbered 0.
    397. 

  397. <li>END - The ending position of the feature in the chromosome or
    398. 

  398.     contig.  This base is not included in the feature.  For example,
    399. 

  399.     the first 100 bases of a chromosome are described as START=0,
    400. 

  400.     END=100, and span the bases numbered 0-99.
    401. 

  401. </ul>
    402. 

  402. Optional:
    403. 

  403. <ul>
    404. 

  404. <li>STRAND - Defines the strand, either '<code>+</code>' or
    405. 

  405. '<code>-</code>'.
    406. 

  406. <li>Header row
    407. 

  407. </ul>
    408. 

  408. Example:
    409. 

  409. <pre>
    410. 

  410.     #CHROM  START  END    STRAND  NAME  COMMENT
    411. 

  411.     chr1    10     100    +       exon  myExon
    412. 

  412.     chrX    1000   10050  -       gene  myGene
    413. 

  413. </pre>
    414. 

  414. <dl><dt>Can be converted to:
    415. 

  415. <dd><ul>
    416. 

  416. <li>BED<br>
    417. 

  417. The exact changes needed and tools to run will vary with what fields
    418. 

  418. are in the Interval file and what type of BED you are converting to.
    419. 

  419. In general you will likely use Text Manipulation &rarr; Compute, Cut,
    420. 

  420. or Merge Columns.
    421. 

  421. </ul></dl>
    422. 

  422. <p>
    423. 

  423. 

  424. <div><a name="lav"></a></div>
    425. 

  425. <hr>
    426. 

  426. <strong>LAV</strong>
    427. 

  427. <p>
    428. 

  428. <a href="http://www.bx.psu.edu/miller_lab/dist/lav_format.html">LAV</a>
    429. 

  429. is the raw pairwise alignment format that is output by BLASTZ.  The
    430. 

  430. first line begins with <code>#:lav</code>.
    431. 

  431. <!-- (not available on Main)
    432. 

  432. <dl><dt>Can be converted to:
    433. 

  433. <dd><ul>
    434. 

  434. <li>BED<br>
    435. 

  435. Convert Formats &rarr; LAV to BED
    436. 

  436. </ul></dl>
    437. 

  437. -->
    438. 

  438. <p>
    439. 

  439. 

  440. <div><a name="lped"></a></div>
    441. 

  441. <hr>
    442. 

  442. <strong>LPED</strong>
    443. 

  443. <p>
    444. 

  444. This is the linkage pedigree format, which consists of separate MAP and PED
    445. 

  445. files.  Together these files describe SNPs; the map file contains the position
    446. 

  446. and an identifier for the SNP, while the pedigree file has the alleles.  To
    447. 

  447. upload this format into Galaxy, do not use Auto-detect for the file format;
    448. 

  448. instead select <code>lped</code>.  You will then be given two sections for
    449. 

  449. uploading files, one for the pedigree file and one for the map file.  For more
    450. 

  450. information, see
    451. 

  451. <a href="http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/input-file-formats-0"
    452. 

  452. >linkage pedigree</a>,
    453. 

  453. <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#map">MAP</a>,
    454. 

  454. and/or <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped">PED</a>.
    455. 

  455. <dl><dt>Can be converted to:
    456. 

  456. <dd><ul>
    457. 

  457. <li>PBED<br>Automatic
    458. 

  458. <li>FPED<br>Automatic
    459. 

  459. </ul></dl>
    460. 

  460. <p>
    461. 

  461. 

  462. <div><a name="maf"></a></div>
    463. 

  463. <hr>
    464. 

  464. <strong>MAF</strong>
    465. 

  465. <p>
    466. 

  466. <a href="http://main.genome-browser.bx.psu.edu/FAQ/FAQformat#format5"
    467. 

  467. >MAF</a> is the multi-sequence alignment format that is output by TBA
    468. 

  468. and Multiz.  The first line begins with '<code>##maf</code>'.  This
    469. 

  469. word is followed by whitespace-separated "variable<code>=</code>value"
    470. 

  470. pairs.  There should be no whitespace surrounding the '<code>=</code>'.
    471. 

  471. <dl><dt>Can be converted to:
    472. 

  472. <dd><ul>
    473. 

  473. <li>BED<br>
    474. 

  474. Convert Formats &rarr; MAF to BED
    475. 

  475. <li>Interval<br>
    476. 

  476. Convert Formats &rarr; MAF to Interval
    477. 

  477. <li>FASTA<br>
    478. 

  478. Convert Formats &rarr; MAF to FASTA
    479. 

  479. </ul></dl>
    480. 

  480. <p>
    481. 

  481. 

  482. <div><a name="mastervar"></a></div>
    483. 

  483. <hr>
    484. 

  484. <strong>MasterVar</strong>
    485. 

  485. <p>
    486. 

  486. MasterVar is a tab delimited text format with specified fields developed
    487. 

  487. by the Complete Genomics life sciences company.  
    488. 

  488. <a href="http://media.completegenomics.com/documents/DataFileFormats_Standard_Pipeline_2.2.pdf"
    489. 

  489. >Field specifications</a>.
    490. 

  490. <dl><dt>Can be converted to:
    491. 

  491. <dd><ul>
    492. 

  492. <li>pgSnp<br>
    493. 

  493. Convert Formats &rarr; MasterVar to pgSnp
    494. 

  494. <li>gd_snp<br>
    495. 

  495. Convert Formats &rarr; MasterVar to gd_snp
    496. 

  496. </ul></dl>
    497. 

  497. <p>
    498. 

  498. 

  499. <div><a name="pbed"></a></div>
    500. 

  500. <hr>
    501. 

  501. <strong>PBED</strong>
    502. 

  502. <p>
    503. 

  503. This is the binary version of the LPED format.
    504. 

  504. <dl><dt>Can be converted to:
    505. 

  505. <dd><ul>
    506. 

  506. <li>LPED<br>Automatic
    507. 

  507. </ul></dl>
    508. 

  508. <p>
    509. 

  509. 

  510. <div><a name="pgSnp"></a></div>
    511. 

  511. <hr>
    512. 

  512. <strong>pgSnp</strong>
    513. 

  513. <p>
    514. 

  514. This is the personal genome SNP format used by UCSC.  It is a BED-like
    515. 

  515. format with columns chosen for the specialized display in the browser
    516. 

  516. for personal genomes.  
    517. 

  517. <a href="http://genome.ucsc.edu/FAQ/FAQformat.html#format10"
    518. 

  518. >Field specifications</a>.  
    519. 

  519. Galaxy treats it the same as an interval file.
    520. 

  520. <p>
    521. 

  521. 

  522. <div><a name="psl"></a></div>
    523. 

  523. <hr>
    524. 

  524. <strong>PSL</strong>
    525. 

  525. <p>
    526. 

  526. <a href="http://main.genome-browser.bx.psu.edu/FAQ/FAQformat#format2">PSL</a>
    527. 

  527. format is used for alignments returned by
    528. 

  528. <a href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start">BLAT</a>.
    529. 

  529. It does not include any sequence.
    530. 

  530. <p>
    531. 

  531. 

  532. <div><a name="scf"></a></div>
    533. 

  533. <hr>
    534. 

  534. <strong>SCF</strong>
    535. 

  535. <p>
    536. 

  536. This is a binary sequence format originally designed for the Staden
    537. 

  537. sequence handling software package.  Files should have a
    538. 

  538. '<code>.scf</code>' file extension.  You must manually select this
    539. 

  539. file format when uploading the file.
    540. 

  540. <a href="http://staden.sourceforge.net/manual/formats_unix_2.html"
    541. 

  541. >More information</a>
    542. 

  542. <p>
    543. 

  543. 

  544. <div><a name="sff"></a></div>
    545. 

  545. <hr>
    546. 

  546. <strong>SFF</strong>
    547. 

  547. <p>
    548. 

  548. This is a binary sequence format used by the Roche 454 GS FLX
    549. 

  549. sequencing machine, and is documented on p.&nbsp;528 of their
    550. 

  550. <a href="http://sequence.otago.ac.nz/download/GS_FLX_Software_Manual.pdf"
    551. 

  551. >software manual</a>.  Files should have a '<code>.sff</code>' file
    552. 

  552. extension.
    553. 

  553. <!-- You must manually select this file format when uploading the file. -->
    554. 

  554. <dl><dt>Can be converted to:
    555. 

  555. <dd><ul>
    556. 

  556. <li>FASTA<br>
    557. 

  557. Convert Formats &rarr; SFF converter
    558. 

  558. <li>FASTQ<br>
    559. 

  559. Convert Formats &rarr; SFF converter
    560. 

  560. </ul></dl>
    561. 

  561. <p>
    562. 

  562. 

  563. <div><a name="table"></a></div>
    564. 

  564. <hr>
    565. 

  565. <strong>Table</strong>
    566. 

  566. <p>
    567. 

  567. Text data separated into columns by something other than tabs.
    568. 

  568. <p>
    569. 

  569. 

  570. <div><a name="tab"></a></div>
    571. 

  571. <hr>
    572. 

  572. <strong>Tabular (tab-delimited)</strong>
    573. 

  573. <p>
    574. 

  574. One or more columns of text data separated by tabs.
    575. 

  575. <dl><dt>Can be converted to:
    576. 

  576. <dd><ul>
    577. 

  577. <li>FASTA<br>
    578. 

  578. Convert Formats &rarr; Tabular-to-FASTA<br>
    579. 

  579. The Tabular file must have a title and sequence column.
    580. 

  580. <li>FASTQ<br>
    581. 

  581. NGS: QC and manipulation &rarr; Generic FASTQ manipulation &rarr; Tabular to FASTQ
    582. 

  582. <li>Interval<br>
    583. 

  583. If the Tabular file has a chromosome column (or is all on one
    584. 

  584. chromosome) and has a position column, you can create an Interval
    585. 

  585. file (e.g. for SNPs).  If it is all on one chromosome, use
    586. 

  586. Text Manipulation &rarr; Add column to add a CHROM column.
    587. 

  587. If the given position is 1-based, use
    588. 

  588. Text Manipulation &rarr; Compute with the position column minus 1 to
    589. 

  589. get the START, and use the original given column for the END.
    590. 

  590. If the given position is 0-based, use it as the START, and compute
    591. 

  591. that plus 1 to get the END.
    592. 

  592. </ul></dl>
    593. 

  593. <p>
    594. 

  594. 

  595. <div><a name="txtseqzip"></a></div>
    596. 

  596. <hr>
    597. 

  597. <strong>Txtseq.zip</strong>
    598. 

  598. <p>
    599. 

  599. A zipped archive consisting of flat text sequence files.  All files
    600. 

  600. in this archive must have the same file extension of
    601. 

  601. '<code>.txt</code>'.  You must manually select this file format when
    602. 

  602. uploading the file.
    603. 

  603. <p>
    604. 

  604. 

  605. <div><a name="vcf"></a></div>
    606. 

  606. <hr>
    607. 

  607. <strong>VCF</strong>
    608. 

  608. <p>
    609. 

  609. Variant Call Format (VCF) is a tab delimited text file with specified
    610. 

  610. fields.  It was developed by the 1000 Genomes Project.
    611. 

  611. <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"
    612. 

  612. >Field specifications</a>.
    613. 

  613. <dl><dt>Can be converted to:
    614. 

  614. <dd><ul>
    615. 

  615. <li>pgSnp<br>
    616. 

  616. Convert Formats &rarr; VCF to pgSnp
    617. 

  617. </ul></dl>
    618. 

  618. <p>
    619. 

  619. 

  620. <div><a name="wig"></a></div>
    621. 

  621. <hr>
    622. 

  622. <strong>Wiggle custom track</strong>
    623. 

  623. <p>
    624. 

  624. Wiggle tracks are typically used to display per-nucleotide scores
    625. 

  625. in a genome browser.  The Wiggle format for custom tracks is
    626. 

  626. line-oriented, and the wiggle data is preceded by a track definition
    627. 

  627. line that specifies which of three different types is being used.
    628. 

  628. <a href="http://main.genome-browser.bx.psu.edu/goldenPath/help/wiggle.html"
    629. 

  629. >More information</a>
    630. 

  630. <dl><dt>Can be converted to:
    631. 

  631. <dd><ul>
    632. 

  632. <li>Interval<br>
    633. 

  633. Get Genomic Scores &rarr; Wiggle-to-Interval
    634. 

  634. <li>As a second step this could be converted to 3- or 4-column BED,
    635. 

  635. by removing extra columns using
    636. 

  636. Text Manipulation &rarr; Cut columns from a table.
    637. 

  637. </ul></dl>
    638. 

  638. <p>
    639. 

  639. 

  640. <div><a name="gd_ped"></a></div>
    641. 

  641. <hr>
    642. 

  642. <strong>gd_ped</strong>
    643. 

  643. <p>
    644. 

  644. Similar to the linkage pedigree format (lped).  
    645. 

  645. <p>
    646. 

  646. 

  647. <div><a name="text"></a></div>
    648. 

  648. <hr>
    649. 

  649. <strong>Other text type</strong>
    650. 

  650. <p>
    651. 

  651. Any text file.
    652. 

  652. <dl><dt>Can be converted to:
    653. 

  653. <dd><ul>
    654. 

  654. <li>Tabular<br>
    655. 

  655. If the text has fields separated by spaces, commas, or some other
    656. 

  656. delimiter, it can be converted to Tabular by using
    657. 

  657. Text Manipulation &rarr; Convert delimiters to TAB.
    658. 

  658. </ul></dl>
    659. 

  659. <p>
    660. 

  660. 

  661. <!-- blank lines so internal links will jump farther to end -->
    662. 

  662. <br><br><br><br><br><br><br><br><br><br><br><br>
    663. 

  663. <br><br><br><br><br><br><br><br><br><br><br><br>
    664. 

  664. </body>
    665. 

  665. </html>
    666.