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  • #16
    disheartening

    It's rather disheartening that this has been a known issue for more than a year and there is still no fix.

    I just switched to DESeq from Cufflinks and am learning my THIRD method of generating the counts matrix to feed into DESeq.

    I'm beginning to wonder if any published bioinfo tools are actually usable in the real world.

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    • #17
      Maybe we just need a more work to sort the bam file according to read name "samtools sort -n"

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      • #18
        It's a really easy fix. Editing my file (yours may be in a different location):
        Code:
        sudo vim +625 /usr/lib64/python2.7/site-packages/HTSeq-0.6.1p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py
        in vim, replace the max_buffer_size default setting (my new setting is bolded):
        Code:
        def pair_SAM_alignments_with_buffer( alignments, max_buffer_size=[B]30000000[/B] ):

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        • #19
          htseq-count bug

          I have tried the above suggestion changing the limit to 30G but still get the same error.

          Any fix yet?
          Last edited by arkanion; 08-19-2016, 10:16 PM. Reason: improved info

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