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Question: how to convert nucleotide strand from BioMart (1, -1) to strands compatible to Galaxy (+, -)
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gravatar for mtjmar002
3.5 years ago by
mtjmar002 • 0
France
mtjmar002 • 0 wrote:

I cannot figure out how to convert strands coordinates downloaded from BioMart (-1, 1) to strands coordinates compatible with Galaxy (-, +) in the c4 column of a BED file. There is a paper saying to compute the expression:

c4==1 and "-" or (c4==1 and "+" or "")

I've tried this and other small variations of this expression but none seems to work.

Can anyone help me pease? It should be the same as in Python...
compute replace text manipulation format dataset • 1.3k views
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modified 3.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.5 years ago by mtjmar002 • 0
1
gravatar for Jennifer Hillman Jackson
3.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

UPDATED:

This can be done in two steps:

  1. Using the tool "Compute an expression on every row", use the term:
    str(int(c4)).replace("-1","-").replace("1","+")
  2. From here, in interval format (the dataset you describe is not really BED format. BED format has strand in the 6th column), one can reassign strand as the 5th column and use the dataset from there with many tools without issue.
  3. Or, using the tool "Cut", pull out just the columns for a 'clean' final interval dataset:
    c1,c2,c3,c5
  4. (Optional) History menu (gear icon): Extract workflow! Edit/label as desired. 

Improved solution via Dan Blankenburg, Galaxy team

Best, Jen, Galaxy team
ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k
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