[mira_talk] Re: trimming for fastq with SANGER quality

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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