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