Hi, galaxy users

How to get Tophat alignment statistics such as % of reads aligned to exon,
intron, splice junction? is there a Log file available?
How many unique and mutiple alignments?
I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none
reported the information I need.

Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645
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