Can you describe it, thank you!
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user191006 •
Unmapped Pairs in Bam file
Hi,
I want to work with unmapped reads in BAM file(generally listed at the end of the file). I can easily collect them with flags. My problem is that I need make indexing for unmapped reads, thank you!
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Devon Ryan
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samtools fastq -f 12 -n -1 read1.fastq -2 read2.fastq input.bam
I presume this needs to be name sorted (samtools sort -n) first.
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Devon Ryan
can you stop being a cuck
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chromosomegun •
The samtools fastq command produces one or more fastq files from a BAM file. The -f 12 option specifies only entries with neither mate mapped.
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What do you mean by "make indexing for unmapped reads"? You can index a BAM file with unmapped reads, that's not an issue.
I want to make an assembly with these unmapped reads for such as insertions etc.