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  • Output of HTseq-count?

    Hi Everyone,
    I'm trying my hands at HTseq-count and was able to run it on our university cluster. We're using version htseq/0.4.6p1. My input command was
    htseq-count --stranded=no -o samout q1.sam GeneWithUTR.gff
    At the end of the run I got following output message,
    43033693 reads processed.
    no_feature 39980188
    ambiguous 0
    too_low_aQual 0
    not_aligned 0
    alignment_not_unique 63473377.
    Is this all that is of the output? I looked for a file with read counts but didn't end up having one. Is there some problem here. I tried to give -o as output string..but to an error message saying that there's no such option. What am I doing wrong?
    Thanks in advance for the answer!
    Best,

  • #2
    As a first step, try to use a current version of HTSeq, please.

    Then, remember that you need to specify the '-i' and '-t' options unless you use an Ensembl GTF file.

    Comment


    • #3
      Hi Simon,
      Thanks a lot for the reply. I'll try the latest version!
      Best,

      Comment


      • #4
        Hi Simon,
        I tried the latest version and also added the attributes..it works now.
        Thanks a lot..
        Best,

        Comment


        • #5
          Hi,

          I'm switching over to try HTSeq to use with DESeq, and I'm having a little trouble getting it to run. Specifically, I'm running it like this:

          python -m HTSeq.scripts.count -o HT_Out accepted_hits.sam hg19_knowngene2.gtf

          I got my accepted_hits.sam file by first sorting by output from Tophat (accepted_hits.bam) and then using samtools view to convert the sorted accepted_hits.bam to a sorted accepted_hits.sam.

          However, every line outputted says the following:
          Warning: Read HWI-1KL118:23:C0J57ACXX:8:1106:5750:192499 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)

          What am I doing wrong?

          Comment


          • #6
            You need to sort by read name before inputting to HTSeq. It seems you have sorted in the "regular way", by genomic coordinates.

            Comment


            • #7
              Thanks, that did the trick!

              Comment


              • #8
                Can I run more than one count table at a time? Sorry, I'm not familiar with Python, so I've been running my HTSeq like this:

                python -m HTSeq.scripts.count -o HT_Out accepted_hits.sam hg19_knowngene2.gtf

                And after I run that on one of my samples, when I go to run it on another, it seems like the first file stopped running.

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                • #9
                  How do you start the multiple processes? Most likely, you have made a mistake that has little to do with Python or htseq.

                  Comment

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