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  • htseq-count output

    Hi,

    Is there an easy way to sort the output from htseq-count based on read count. I have mapped my SAM-file onto miRNA-GFF file and basically I want a 2 column output with miRNA and count-number.

    Best

  • #2
    Look at the man page for sort:

    sort -grk2 htseq.out

    Comment


    • #3
      I didnt find it, or maybe I didnt get you?
      Where?

      Comment


      • #4
        At the unix command line, type:

        man sort

        Comment


        • #5
          and -grk2 is?

          When I run htseq-count the reads get sorted in the command line summary, but not in the output. I basically want what gets printed in the terminal when htseq-count is done.

          Comment


          • #6
            Read the man page for sort and you'll see what -grk2 does.

            You have to run the sort command on the output you get from htseq-count. Or else pipe the output to sort.

            Comment


            • #7
              Didnt work. Output from sort -grk2 <input_file> was the same as my input. nothing happened.

              Comment


              • #8
                It should have. I did this on some htseq-count data of my own. I didn't remove the last four lines, that's why the alignment_not_unique and no_features are showing up.


                Code:
                sdt5z@host:~/htseq$ head gm.htseq.txt 
                1/2-SBSRNA4	0
                A1BG	0
                A1BG-AS1	0
                A1CF	0
                A2LD1	0
                A2M	0
                A2ML1	0
                A2MP1	0
                A4GALT	0
                A4GNT	0
                
                sdt5z@host:~/htseq$ sort -grk2 gm.htseq.txt |head
                EEF2	19280
                alignment_not_unique	15890
                no_feature	6321
                AES	6173
                MKNK2	5681
                AP3D1	3406
                OAZ1	3385
                TCF3	3160
                MOBKL2A	2791
                BSG	2655
                Try separating the arguments (sort -g -r -k2 infile.txt)

                Comment

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