Hi!,
This should be very easy but it's confusing to me. I would appreciate some help. I have paired end Illumina sequencing. I want to keep only *unmapped* reads. Additionally, if one of the mates mapped I do NOT want to keep that pair either. I want to use unmapped reads for assembly. I am running following samtools flag, am I doing the right thing?
If this is the right command, why my output.sam file has reads with chromosome names on it. Thank you very much.
This should be very easy but it's confusing to me. I would appreciate some help. I have paired end Illumina sequencing. I want to keep only *unmapped* reads. Additionally, if one of the mates mapped I do NOT want to keep that pair either. I want to use unmapped reads for assembly. I am running following samtools flag, am I doing the right thing?
Code:
samtools view -f4 -F8 -S input.sam > output.sam
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