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Old 05-26-2013, 06:49 PM   #1
vivienne_lovely
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Unhappy extrat unaligned reads from unmapped.bam (tophat)

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?
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Old 05-26-2013, 10:58 PM   #2
swbarnes2
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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

Code:
samtools view -f 4 sort.bam > unmapped.bam
Will pull unmapped reads out of a .bam that has unmapped reads in it.
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