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prewer93 / ea-utils

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The gtf2bed script generate bed with wrong chrStart and chrEnd coordinates for plus strand #28

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
BED format cover the region [chrStart, chrEnd).
But when I checked the output BED and compared with GTF (which covers 
[left,right] region), what the BED represented are always (chrStart, chrEnd], 
which is fine for minus but not for plus strand.

Original issue reported on code.google.com by hy11...@gmail.com on 4 Mar 2014 at 4:04

GoogleCodeExporter commented 8 years ago 
Sorry for not following the questions, but I think it's easy for you to check, 
:)

Original comment by hy11...@gmail.com on 4 Mar 2014 at 4:05

GoogleCodeExporter commented 8 years ago 
I just downloaded mm10 gtf and bed from ucsc and i find no discrepencies.   In 
fact, you can sort it and do a diff and see that there are no issues.

Original comment by earone...@gmail.com on 4 Mar 2014 at 5:23

GoogleCodeExporter commented 8 years ago 
Opps, gtf is 1-based. I should have checked with ucsc files like that.
Sorry for taking your time, and thanks for the nice script.

Original comment by hy11...@gmail.com on 5 Mar 2014 at 2:56

GoogleCodeExporter commented 8 years ago

Original comment by earone...@gmail.com on 17 Mar 2014 at 7:10