ty of mapping is not
changed?
Best,
Jianguang
From: Jeremy Goecks [jeremy.goe...@emory.edu]
Sent: Wednesday, April 10, 2013 3:16 PM
To: Du, Jianguang
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Are reads of 36nt in length long enough to accuta
> I have one more question about the "Anchor length". For a RNA-seq read mapped
> on the splicing junction under the 0 mismatch condition, if 5 nucleotides of
> one end map on one exon, does it mean the rest part of the read must map on
> the adjacent exon? What I want to understand is that, al
> 1) My reads are 36nt long. How much should I set for "the Minimum length of
> reads segments" to get the most reliable output with the highest mapping of
> splicing junctions?. In my previous run of TopHat, I set it as 18. Can I
> reduce it more to get better mapping on splicing junctions?
Yo
y Goecks [jeremy.goe...@emory.edu]
Sent: Tuesday, April 09, 2013 1:57 PM
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?
In addition to reducing the "the Minimum length of reas segm
> 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?
Definitely worth a try.
> Looks like the setting for "Anchor length" only affects the number of mapped
> splicing junctions reported in the .
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 t
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,
J.
On Apr 8, 2013, at 5:45 PM, Du, Jianguang wrote:
> Hi
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 para
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