[mira_talk] Re: Which reads to use from debrislist to the novo analysis?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 7 May 2015 21:07:19 +0200
On 07 May 2015, at 16:39 , Dietmar Fernandez <dietmar.fernandez@xxxxxxxxxxxx>
wrote:
After doing first a mapping afterwards I got the debrislist file and four
different types of reads where found.
NO_OVERLAP
CLIP_BAD_SOLEXA_END
CLIP_KNOWNADAPTORRIGHT
CLIP_POLYBASEATEND
CLIP_PROPOSEDENDCLIP
NOT_MAPPED
I wonder which of the reads should I use for performing a de novo analysis in
order to detect sequences not present in the reference strain. I think I
should just use "NO_OVERLAP" and "NOT_MAPPED" reads. Is this correct? What
is the difference between this two types of sequences?
This is correct.
The differences are minor for what you plan to do. NO_OVERLAP means that the
read passed a first kmer matching step (SKIM filter), but then did not pass the
Smith-Waterman alignment step. Reads having NOT_MAPPED passed SW, but were
somehow still rejected from being finally mapped in the contig alignment.
B.
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