[mira_talk] Re: trimming for fastq with SANGER quality
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 14 Mar 2012 19:47:10 +0100
On Mar 14, 2012, at 15:27 , Christoph Hahn wrote:
> I recently got some fresh data from the Illumina hiseq. I did a quick mapping
> assembly with Mira. Afterwards the plan was to extract the Mira trimmed reads
> from the readpool.maf file (as discussed in a previous mail). When I looked
> at this reads I discovered that MIRA did no trimming at all. I dont think the
> read quality is that good.
Oh, MIRA probably did trim, at least if the parameter -CL:pec was set to "on"
(which is the default anyway).
When converting the MAF file, you probably said "give me all the sequences in
the MAF file" and convert_project dutifully obliged. What you should have said
is "give me all the sequences, but clipped" :-)
convert_project -C ...
> The hiseq reads come in SANGER fastq quality format, as far as I can say
> (waiting for the reply from the sequencing facility). I found the
> [fastq_qualoffset(fqqo)=integer] switch in the manual but it also says that
> MIRA is capable of guessing the right format correctly.. Shall I just run it
> again with fqqo=33, or is there something else wrong?
No need to rerun and very probably nothing wrong.
B.
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