How to get statistics data from sam/bam file generated by trinity packages

[taoxiang180]

I have assemblied a great set of Illumina reads and aligned them back to the contigs by trinity, but i can't find any statistics data for the mapping results in the output file, I just want to investigate the rate of mapped/unmapped reads, which tools can do this? and how it work?
Any pointers will be appreciated.
Thanks!

[dariober]

I just want to investigate the rate of mapped/unmapped reads, which tools can do this? and how it work?
Any pointers will be appreciated.
Thanks!

The easiest way is probably with samtools:

samtools flagstat myaln.bam

For RNAseq a very comprehensive report is produced by RNA-SeQC https://confluence.broadinstitute.or...Tools/RNA-SeQC

Best
Dario