Issue with alignment report

[P M]

Hi

I am a novice in RNA-seq. I am using Sammate to generate alignment report (read distribution report) from RNA-seq data that was aligned with Tophat. However, the report shows that 0% of the reads mapped to junctions and intergenic region. I have never gotten such results in the past when I was analysing other sets of data. I think there might be something wrong with the alignment. When viewing the bam files in IGV, I do see reads that span junctions. I would really appreciate if you could help me with this. 

Thanks

P

[Tin Chi Nguyen]

Hi,

Can you provide more details on parameters used in SAMMate? I can debug it if you also provide the data you run on.

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From: "P M" <prakriti...@gmail.com>
To: asam...@googlegroups.com
Sent: Wednesday, January 9, 2013 12:57:38 PM
Subject: Issue with alignment report