On Tue, May 24, 2011 at 12:40 AM, Aaron Jex <ajex@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. Peter