Are bam2fastq --no-aligned and samtools fastq -f 4 same?
hi i am trying to explore the unmapped reads of my genome assembly. I straight forward tried samtools fastq -f 4 bla.bam > unmapped.fq but it gave me single file which was unusable for contig generation using spades. So i shifted to bam2fastq --no-aligned. Although i got things working but i am not pretty sure if both approach are same and are right to extract unmapped reads only.
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Pierre Lindenbaum
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Yogesh •
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1) samtools sort -n or samtools collate must be called before samtools fastq
2)
see option
-1and-2