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Old 11-08-2011, 01:16 AM   #1
mapardo
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Location: Spain

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Default htseq count missing last mapped fragment

I am using the program htseq-count v0.5.3 with an standard sam file from the mapping of a set of paired end reads. Comparing this file with the output file that can be obtained with the option '-o', I've realized that the mapping for the last fragment (two lines) is missing. Furthermore, I check the resulting count and one mapping is missing as well.

Has anybody got the same results? Is there any fix to solve this?

Thank you.
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Old 11-08-2011, 03:48 AM   #2
Simon Anders
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Quote:
Originally Posted by mapardo View Post
I am using the program htseq-count v0.5.3 with an standard sam file from the mapping of a set of paired end reads. Comparing this file with the output file that can be obtained with the option '-o', I've realized that the mapping for the last fragment (two lines) is missing. Furthermore, I check the resulting count and one mapping is missing as well.
This is a bug, which I fixed a few months ago, in version 0.5.3p1. (Thanks go to Justin Powell who noticed the bug first and even sent me a patch.)
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Old 11-08-2011, 05:27 AM   #3
mapardo
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Sorry. I didnt realize that I was using a version that wasnt updated. Thank you both.
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