[mira_talk] Re: FASTA WITH QUALITY VALUES
- From: Andrej Benjak <abenjak@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 25 Feb 2014 16:20:47 +0100
why QIIME? miraconvert can produce fastq files...
andrej
haven't used MGRAST but I presume you need fastq, python stript from
QIIME should do that from fasta and qual files
http://qiime.org/scripts/convert_fastaqual_fastq.html
Veljo
On 02/25/2014 04:03 PM, Lionel Guy wrote:
Yes.
>From the manual
(http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_res_resultsdir):
The *_d_results directory [...]
• projectname_out.unpadded.fasta: as above, this file contains
as FASTA sequence the consensus of the contigs that were assembled in
the process, put positions in the consensus containing gaps were
removed. The computed consensus qualities are in the corresponding
projectname_out.unpadded.fasta.qual file.
Lionel
On 25 Feb 2014, at 14:58 , Chayan Roy <chayan.roy93@xxxxxxxxx> wrote:
Hii
I have performed an assembly on deep sequenced metagenome. Now i
want to extract contigs larger than 1000. If i have to submit them
in MGRAST i also need the quality values. I am not sure how to do
this. I went through the manual and know how to use the
convert_project to extract contigs >1000 but dont know how add
quality values on them. Will file.unpadded.fasta.qual will serve my
purpose??
Any help..
Mira version: MIRA V3.4.0.1 (production version).
Best
--
CHAYAN ROY
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