[mira_talk] Re: Debris list classification
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 2 Apr 2015 21:01:27 +0200
On 31 Mar 2015, at 17:35 , Hélène Boulain <helene.boulain@xxxxxxxxx> wrote:
[…]
Does it make a difference if I search my expressed genes with contigs
(contigs+singlets with options AS:mrpc=1 and -OUT:sssip=yes) or with contigs
+ no_overlapping reads extracted from the debris list ?
It could make a difference, albeit I expect it to be very small.
I’d like restate what has already been said earlier in this thread: be *very*
careful with the interpretation of reads in the debris file. MIRA is pretty
merciless in throwing away everything which is not supported by enough evidence
of being correct. In ESTs, this unfortunately hits very lowly expressed genes
or splice variants, but they are then indistinguishable from PCR / library-prep
/ sequencing errors.
B.
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