Question: select -500 from the TSS to +500 after the TES strand +/-
0
gravatar for Lila M
22 months ago by
Lila M 410
UK
Lila M 410 wrote:

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!

tss tes coverage sequencing strand • 602 views
ADD COMMENTlink modified 22 months ago by Alex Reynolds26k • written 22 months ago by Lila M 410
0
gravatar for Alex Reynolds
22 months ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

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.)

ADD COMMENTlink written 22 months ago by Alex Reynolds26k

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!

ADD REPLYlink modified 22 months ago • written 22 months ago by Lila M 410
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