extrat unaligned reads from unmapped.bam (tophat)

[vivienne_lovely]

Hi guys,
I want to extract unaligned paired reads from unmapped.bam(tophat output) in fastq fomat, is there any easy way to get those reads?

[swbarnes2]

I think there is a setting on TopHat that will output the unmapped reads to a separate file; I thought that by default, Bowtie will not output them.

In general, unmapped reads will have the 4 flag set in the .bam, so something like

samtools view -f 4 sort.bam > unmapped.bam

Will pull unmapped reads out of a .bam that has unmapped reads in it.