[mira_talk] Re: trimming for fastq with SANGER quality
- From: Christoph Hahn <chrisi.hahni@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 14 Mar 2012 23:22:52 +0100
That was it, thanks!
cheers,
Christoph
On 03/14/2012 07:47 PM, Bastien Chevreux wrote:
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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