On 21/11/13 01:43 PM, Rick White wrote:
> Hello,
>
> For MG-RAST upload it has two problems from Ray outputs.
>
> The space between contig and number with unique sequence number for example.
> >contig-3000000**508 nucleotides
>
> And, it needs coverage information for
> >sequence_number_1_*[cov=2]*
> CTAGCGCACATAGCATTCAGCGTAGCAGTCACTAGTACGTAGTACGTACC
> >sequence_number_2_*[cov=4]*
> ACGTAGCTCACTCCAGTAGCAGGTACGTCGAGAAGACGTCTAGTCATCAT
>
> I was wondering if there was a quick command to add the coverage information
> to the contig file and remove the space.
>
The mode coverage is available in:
RayOutput/
BiologicalAbundances/
_DenovoAssembly/
Contigs.tsv
You would probably need more than a awk command to rewrite the headers though.
>
> Cheers and many thanks
> Rick
> --
> Richard Allen White III M.S.
> PhD Candidate - Suttle Lab
> Department of Microbiology & Immunology
> The University of British Columbia
> Vancouver, BC, Canada
> cell. 604-440-5150 <tel:604-440-5150>
> http://www.ocgy.ubc.ca/~suttle/ <http://www.ocgy.ubc.ca/%7Esuttle/>
>
>
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