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? 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. Best regards, Aaron Aaron Jex, BSc, PhD Senior Research Officer, Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030 tel: +61 3 9731 2294
Aaron, As far as I remember MIRA....isn't MIRA taking into account the low/high quality bases anyway? So no need to filter there right? Only filtering needed is for contaminating sequences.....(incl adapters and such). You can/have to check the MIRA website to be sure though. The high qual segments I have used as in the metagenomics example but indeed you loose the exact qual info....but that is already above the provided threshold (default above 20 in Sanger quality score range). Alex Van: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] Namens Aaron Jex Verzonden: dinsdag 24 mei 2011 1:40 Aan: galaxy-user@bx.psu.edu Onderwerp: [galaxy-user] (no subject) 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? 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. Best regards, Aaron Aaron Jex, BSc, PhD Senior Research Officer, Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030 tel: +61 3 9731 2294
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
participants (3)
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Aaron Jex -
Bossers, Alex -
Peter Cock