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  • How to run HTSeq with paired end file

    I have one paired end SAM file generated by Novoalign. The two ends of one pair share the same read ID, but the HTSeq reports all of them as "alignment_not_unique" and ignores them. Anybody know how to fix this issue? I used the following command,

    htseq-count --stranded=no --mode=intersection-nonempty -t exon -i gene_id inputFile.sam Homo_sapiens.GRCh37.67.chr.gtf > inputFile.htseq.count

    The following are 4 example reads.

    HWI-ST1189:59:C1305ACXX:5:1101:10000:108281 99 chrM 7910 3 51M = 8156 0 CGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACA
    TACTTCCCCC CCCFFFFFHHHHHJJJJJIJJJJIIJJIJJJJJJJIIHFHHHHFFFFFFED PG:Z:novoalignMPI NH:i:2 HI:i:1 AM:i:70 NM:i:0 SM:i:70 GN:Z:585 T
    N:Z:ENST00000361739 ZN:i:2 PQ:i:6 UQ:i:6 AS:i:6 ZS:Z:R
    HWI-ST1189:59:C1305ACXX:5:1101:10000:108281 147 chrM 8156 3 51M = 7910 0 GGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACC
    ACAGTTTCAT IJJJHIJJIJJJJIJJJJJJJJJJJIIJJJJJJJJIIIHHHHHFFFFFCCC PG:Z:novoalignMPI NH:i:2 HI:i:1 AM:i:70 NM:i:0 SM:i:70 GN:Z:585 T
    N:Z:ENST00000361739 ZN:i:2 PQ:i:6 UQ:i:0 AS:i:0 ZS:Z:R
    HWI-ST1189:59:C1305ACXX:5:1101:10000:12609 163 chr6 74229694 1 51M = 74229740 0 CCCGAATCTACGTGTCCAATGACGA
    CAATGTTGATATGAGTCTTTTCCTTT CCCFFFFFHHHHHIIJJJJIJJJJJJJJIJIIJJJJJJJJHIJJJJJIJJF PG:Z:novoalignMPI NH:i:3 HI:i:1 AM:i:70 NM:i:0 SM:i:70 G
    N:Z:1151 TN:Z:ENST00000309268 ZN:i:3 PQ:i:9 UQ:i:0 AS:i:0 ZS:Z:R
    HWI-ST1189:59:C1305ACXX:5:1101:10000:12609 83 chr6 74229740 1 40M943N11M = 74229694 0 CCTTTCCCATTTTGGCT
    TTTAGGGGTAGTTTTCACGACACCTGTGTTCTGG IJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJIIHDHHHHFFFFFCCC PG:Z:novoalignMPI NH:i:3 HI:i:1 AM:i:70 NM:i:0 S
    M:i:70 GN:Z:1151 TN:Z:ENST00000309268 ZN:i:3 PQ:i:9 UQ:i:9 AS:i:9 ZS:Z:R XS:A:-

    Thanks in advance!
    Last edited by xuguorong; 10-26-2012, 04:15 PM.

  • #2
    Nobody knows how to run HTSeq with paired-end reads?

    Comment


    • #3
      Umm, well none of those reads uniquely aligned, so I'm not sure what else you would expect. Note the ZS, ZN, and NH flags, as well as the alignment scores.

      Comment


      • #4
        Thank you so much, dpryan!
        I fixed this issue after improving the unique mapping rate!

        Comment

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