[mira_talk] Re: Why so many sequences in debris file?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 27 May 2011 23:09:14 +0200
On Monday 23 May 2011 21:55:47 jyotsna guleria wrote:
> After taking singlets into account, I am still getting one fourth of my
> sequences in debris. I couldn't figure this out as quality scores for those
> sequences are good and read length as well.
>
> Can anyone help me here?
You might find
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_contigs_singlets_debris
to give you some information why things land in debris. Have a look at the
tmp/log file called <projectname>_int_clippings.0.txt and grep for read names
there.
> Please someone suggest me what to do to avoid getting too many sequences in
> debris or help me understanding debris file in detail.
Have you looked at the debris "by hand" and judged whether they would be useful
to the assembly? Easiest thing to do would be to run BLAST/fasta36 (the
program) with a couple of sequences of the debris against some contigs of MIRA
and see whether you deem them to be useful. They're probably not, but maybe
MIRA was set up too strict and feedback on that is always welcome.
B.
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