This is a test version of Biostars. For the public version, visit https://www.biostars.org.
select -500 from the TSS to +500 after the TES strand +/-

Hi everybody! Hi have a terrible doubt, I want to select the coverage over -500 from the TSS to +500 after the TES, from my bed file :

  $1        $2         $3        $4
chr1   genestart    geneend    strand
chr1    12627939    12676788     -
chr1    17185444    17185516     -
chr1    17248445    17299474     +
chr1    19974104    19984949     +

For the strand (+) I've used the next command $2-500 $3+500 but when I get the values for strand (-) I have doubt, I think that it should be $2+500 $3-500, is that right?

Thank you!

sequencing strand tss tes coverage
• 2,076 views • link
updated by Alex Reynolds Alex Reynolds • written by Lila M Lila M

1 answer

No, it would be the same shift regardless of strand, in this case. (Short of one-off issues that would be due to any signal or nucleotide patterns that may be measured downstream, that is.)

• 0 views • link
written by Alex Reynolds Alex Reynolds

So for the strand + and - should be $2-500 $3+500?

Original

chr1   genestart    geneend    strand
chr1    12627939    12676788     -
chr1    17185444    17185516     -
chr1    17248445    17299474     +
chr1    19974104    19984949     +

Result

chr1   genestart    geneend    strand
chr1    12627439    12677288 -
chr1    17184944    17186016 -
chr1    17247945    17299974 +
chr1    19973604    19985449 +

Is that right?

Thanks!

• 0 views • link
written by Lila M Lila M

Log in to answer this question.

More posts like this