[mira_talk] Re: 454 read mapping problem
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 1 Jun 2014 21:53:41 +0200
On 31 May 2014, at 21:17 , Cécile Gracianne <cecile.gracianne@xxxxxxxxx> wrote:
> I am running a mapping running with 454 reads on 11 sequences of reference. I
> am using mira 4.0.2 on mac.
> Mira reads the data file and the manifest but stop before to start the
> mapping. I have no idea why.
MIRA clipped all your reads back to a length of 0. That may have several causes:
1. the sequences of your reads are all lower case. Though in this case MIRA
should’ve given another warning.
2. the sequences of your reads contain lots and lots (and extremely lots) of
sequencing errors. Quite improbable, but possible.
3. the sequences of your reads are very low coverage AND do not match the
reference sequence.
Have a look at the “*clipping*” log files in the temporary directory of MIRA to
find out what happened.
B.
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