[mira_talk] Re: Too many redundant contigs
- From: Daniela Dias Xavier <dani_xavier@xxxxxxxxxxx>
- To: mira <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 16 Jan 2012 12:38:54 +0000
Thank you all!
You helped me a lot.
Cheers
Dani.
From: bach@xxxxxxxxxxxx
Subject: [mira_talk] Re: Too many redundant contigs
Date: Fri, 13 Jan 2012 21:02:12 +0100
To: mira_talk@xxxxxxxxxxxxx
On Jan 13, 2012, at 14:19 , Sven Klages wrote:2012/1/13 Remo Sanges
<noncoding@xxxxxxxxx>
What I find useful when I want to reduce redundancy is to use the output
of mira (.unpadded.fasta + .unpadded.fasta.qual) as input for cap3.
Well, ok, why not. Personally I'd not go that way. But IMHO it is still quite
important, to find out what "redundant " really means.
Just parts of contigs with homologies? Or some artefacts from library
construction in the sequencing library
(we used a kind of custom approach years ago, I needed to individually clip
these remainders)?
Both approaches have their pros and cons. At work I do have some RNASeq
libraries to analyse and the biologists are sometimes appalled by the number of
mutations present in the data. Of course, each and every one must be analysed
in-depth because it could be important *sigh*
When she (roughly) knows why these contigs are not merged, she can start to
alter assembly strategy accordingly.
Or simply continue with the data as it is. Doing a condensing too early is
sometimes a bit dangerous :-)
B.
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