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htseq count missing last mapped fragment

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  • 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.

  • #2
    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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    • #3
      Sorry. I didnt realize that I was using a version that wasnt updated. Thank you both.

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