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https://bitbucket.org/cistrome/cistrome-harvard/
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 1
 2HELP
 3====
 4
 5**What to do if I have a problem?**
 6
 7E-mail us at `galaxy@bx.psu.edu`__
 8
 9.. __: mailto:galaxy@bx.psu.edu
10
11-----
12
13**What do I do first?**
14
15To start your Galaxy session you first need to initialize history by adding some data. You can do this by using *Data* tool on the laft pane of the Galaxy window.
16
17Once you have at least one item in the history, you will be able to run appropriate tools.
18
19-----
20
21**Datatypes**
22
23Galaxy supports the following datatypes:
24
25 * text - any text file
26 * tabular - tab delimited text
27 * interval - tab delimited file containing information about genome features
28 * BED - a special case of the interval type
29 * FASTA - nucleotide or protein sequences
30 * AXT - blastZ-style pairwise alignments
31 * MAF - TBA and multiZ multiple alignments
32
33-----
34
35**What is the difference between Interval and BED?**
36
37`BED format`__ always contains *chromosome*, *start*, and *end* as the first three fields. Interval is more generic and does not require these fields to be in any strict order.  Here is the formal description of interval format used in Galaxy:
38
39.. __: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
40
41- Tab delimited format
42- File must start with definition line in the following format (columns may be in any order).::
43
44    #CHROM START END STRAND
45
46- CHROM - The name of the chromosome (e.g. chr3, chrY, chr2_random) or contig (e.g. ctgY1).
47- START - The starting position of the feature in the chromosome or contig. The first base in a chromosome is numbered 0.
48- END - The ending position of the feature in the chromosome or contig. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
49- STRAND - Defines the strand - either '+' or '-'.
50- Example.::
51    
52    #CHROM START END   STRAND NAME COMMENT
53    chr1   10    100   +      exon myExon
54    chrX   1000  10050 -      gene myGene     
55 
56