Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data?
Thanks
Thanks
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There are quite a few ways depending on what software you have.
I would recommend using either bamtools stats or Picard's CollectRnaSeqMetrics to get some more information. -
On the accepted_hits.bam, run Picrads, SortSam.jar, BuildbamIndex.jar, ReorderSam.jar and CollectAlignmentMetrics.jar in order. The resultant metrics file has alignment stats.Comment
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