Hi Jeremy,

Thank you for the information.

In addition to reducing the "the Minimum length of reas segments", do I also need to reduce "Anchor length" to get more mapping on splicing junctins?

Looks like the setting for "Anchor length" only affects the number of mapped splicing junctions reported in the .splicing junctions output. Is my understanding correct? Does the "regions" mean the number of mapped splicing junctions?

Thanks.

Best,

Jianguang

From: Jeremy Goecks [jeremy.goecks@emory.edu]
Sent: Tuesday, April 09, 2013 9:03 AM
To: Du, Jianguang
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Are reads of 36nt in length long enough to accutatly map on splicing junctions?

36bp reads will map across splice junctions but at a relatively low rate; you can try changing segment length to get better mapping, but you'll want to evaluate the results carefully to ensure that you're getting good results.

Good luck,

On Apr 8, 2013, at 5:45 PM, Du, Jianguang wrote:

Hi All,

I have a very basic question. I have RNA-seq datasets of several cell types and want to compare the alternative splicing events between cell types. The reads are 36nt in length. Are these reads long enough to map on the splicing jucntions accurately when I run Tophat with stringent parameters (no mismatch)?

Thanks.

Best,

Jianguang Du

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