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Old 01-14-2013, 07:01 AM   #3
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Originally Posted by marcowanger View Post
I remember Bam2fastq only export read pair. So, all singleton mapped will be discarded. In your case, it may be better to write a small script to parse the singleton out
Are you certain about the singletons thing? It would make sense, butl I just did some checking there with samtools flagstat and according to the numbers I'm looking at for this one accepted_hits.bam file from tophat there were more singleton reads then there were reads discarded by bam2fastq (~3 million more). So if bam2fastq doesn't export singletons, what happened to those 3 million reads.

Actually there are options in tophat for setting it so that there should be no singletons, hopefully that'll fix this.

Last edited by Derek-C; 01-14-2013 at 07:29 AM.
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