User: Flavia

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Flavia0
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Posts by Flavia

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Comment: C: mapped/unmapped mate with samtools
... So.. looking at the unmapped file I found (for example) this couple of reads: HWI-ST1210:100:D19M1ACXX:6:1103:9250:71414    103    CL282Contig2    975    29    87M2I7M    CL282Contig5    647    0    AAAAGGCTAAAGGACAGACCGCACTGTCAACCTCCATACCCGTGCACTCAACGCTATCAACGTACAACAACTACAAGAAACAACGATACGTTCAAC     ...
written 4.6 years ago by Flavia0
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Comment: C: mapped/unmapped mate with samtools
... the unmapped mates are 1453574; the mapped mates 1418724. so I have a difference of 34850..quite significant, I think. ...
written 4.6 years ago by Flavia0
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Comment: C: mapped/unmapped mate with samtools
... I don't think. I did the alignment and then I converted sam in bam samtools view -bS in.sam > out.bam. that's it. ...
written 4.6 years ago by Flavia0
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Comment: C: mapped/unmapped mate with samtools
... oh sorry..in the post I inverted the code for mapped/unmapped!! however ..with -f 0x800 I obtain 0.. but I don't know the meaning ...
written 4.6 years ago by Flavia0
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mapped/unmapped mate with samtools
... Hi, I'm kind of newbie about BWA and I have a trivial question. I performed an alignment with paired reads and now I'm trying to extract some of them with samtools. 1) mapped reads whose mate is unmapped (samtools view -f4 -F8 in.bam) 2)unmapped reads whose mate is mapped (samtools view -f8 -F4 ...
paired reads mapped unmapped samtools bwa written 4.6 years ago by Flavia0

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