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  • htseq-count error with tophat input

    Hi all
    When using htseq-count with sam-files from tophat and gff files from cufflinks, i got following error:

    Error occured in line 1 of file /home/ubelix/sm/mm08c348/counts/ilc31se.sorted.sam.
    Error: Strand must be'+', '-', or '.'.
    [Exception type: ValueError, raised in _HTSeq.pyx:72]

    cmd: htseq-count -t transcript -i ID -s no file.sam cufflinks.gff' > htseq-count

    I checked for the strands in gff file, they look ok (either . - or +). sam file was sorted using sort -n on the bam precursor, so should be ok.
    Any help on this issue would be appreciated!!
    Thank you!
    Michel

  • #2
    I'm currently having exactly same error for name-sorted SAM version of tophat generated BAM file.

    How did you solve this problem then?

    Comment


    • #3
      Hello,

      I am having the same problem. Here is the error and the first line of the file in question (paths redacted):

      Error occured in line 1 of file HC25_4-1_ZT02_1_combined_2.sam.
      Error: Strand must be'+', '-', or '.'.
      [Exception type: ValueError, raised in _HTSeq.pyx:71]

      head -1 HC25_4-1_ZT02_1_combined_2.sam

      HWI-ST1083:106:C1G1MACXX:2:1113:20418:56674:1:N:0:GTGAAA 272 chr2L 49M * 0 0 GACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCAT hhiihhfgcggfiiihiifhhiiiihihhiiiiiiigggggeeeeebb_ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:49 YT:Z:UU NH:i:20 CC:Z:= CP:i:4124 HI:i:0


      Any advice on the matter would be appreciated.

      Comment


      • #4
        GFF files contain strand information as '+' and '-', SAM files don't. Maybe you have passed the two file names in the wrong order.

        Comment


        • #5
          Originally posted by alanlhutchison View Post
          Hello,

          I am having the same problem. Here is the error and the first line of the file in question (paths redacted):

          Error occured in line 1 of file HC25_4-1_ZT02_1_combined_2.sam.
          Error: Strand must be'+', '-', or '.'.
          [Exception type: ValueError, raised in _HTSeq.pyx:71]

          head -1 HC25_4-1_ZT02_1_combined_2.sam

          HWI-ST1083:106:C1G1MACXX:2:1113:20418:56674:1:N:0:GTGAAA 272 chr2L 49M * 0 0 GACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCAT hhiihhfgcggfiiihiifhhiiiihihhiiiiiiigggggeeeeebb_ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:49 YT:Z:UU NH:i:20 CC:Z:= CP:i:4124 HI:i:0


          Any advice on the matter would be appreciated.
          I suspect that you're putting the SAM file were the annotation file should go. The SAM file goes before the annotation file in the command.

          Comment

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