[mira_talk] Mixed case Roche 454 data and -CL:lowercase_clip
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 17 Nov 2009 12:01:56 +0000
Dear Bastien et al,
As you know the Roche SFF tools and sff_extract will output mixed case
sequences, where the good sequence is in upper case, and the start and
end sections are in lower case (indicating adaptors or poor quality
sequence to be trimmed off). This means the case information records
the start/end trim points from the original SFF file.
Back on 1 Oct 2009, you mentioned you had introduced a new clipping
function, -CL:lowercase_clip which would be on by default for 454
data, off otherwise:
//www.freelists.org/post/mira_talk/454-genome-assembly,10
Should this give the same results as following the walk-through recipe
using sff_extract to turn an SFF file into FASTA, QUAL, and an XML
file with the trimming information?
http://chevreux.org/uploads/media/mira3_454dev.html
I'd like to try this on Roche 454 data using either mixed case FASTA
files with QUAL files, or with mixed case FASTQ files. My reason for
wanting to do this is trying out different trimming and filtering
strategies and producing FASTA+QUAL or FASTQ files is easy, while the
XML file is a hassle. Also, being able to give MIRA a single mixed
case FASTQ file seems much more elegant than a bundle of three files
(FASTA, QUAL, XML) which must all be named in a particular way.
However, it seems quite complicated because I have to explicitly turn
off the XML trace info check (using MIRA 3rc4 on Mac OS X):
These fail:
$ mira -job=denovo,genome,accurate,454 454_SETTINGS -fastq=reads.fastq
$ mira -job=denovo,genome,accurate,454 454_SETTINGS -fastq=reads.fastq
-CL:lowercase_clip
Whereas this runs (it is still processing right now - I'm waiting to
see how it compares to the earlier assembly I did using the
FASTA+QUAL+XML version of the same 454 reads):
$ mira -job=denovo,genome,accurate,454 454_SETTINGS -fastq=reads.fastq
-CL:lowercase_clip -LR:mxti=no
This confuses me since the documentation here says mxti defaults to no:
http://chevreux.org/uploads/media/mira3.html
Peter
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