On Tue, May 24, 2011 at 12:40 AM, Aaron Jex <a...@unimelb.edu.au> wrote:
> Hi,
> Can’t seem to find an answer to this on your wiki site and it’s not in the
> tutorial.  I would like to filter my 454 reads for high quality regions,
> rename the resulting sequence fragments AND relink the new reads (fragments)
> to the original quality data so that I can take these filtered reads and
> assembly them using MIRA. Is there a way to do this with Galaxy?

See Alex's answer.

> So
> basically all I want to do is take the new read fragments I get from
> converting the tabular file to the fasta file as shown in your metagenomics
> tutorial, and generate a corresponding qual file for these ‘new’ reads.

When working in Galaxy, I use the SFF converter tool to make FASTQ
rather than FASTA and QUAL.

MIRA will also read in FASTQ, and I find that is easier to work with
for filtering and trimming than a matched FASTA and QUAL file.


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