Hello Soetkin,
Is your concern that the sequences will be in FASTA format (without quality scores) instead of FASTQ format? If so, the Galaxy tool "NGS: QC and manipulation -> Combine FASTA and QUAL into FASTQ" can create placeholder quality values in a FASTQ file appropriate for use with NGS mapping tools.
Hopefully this helps. If you would like further help, please explain the issue in more detail and consider sending a small sample of the data pasted into the email (10 or so entries) if that is relevant.
For reference: http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions
Thanks for using Galaxy!
Jen Galaxy team
On 11/15/11 1:56 AM, Soetkin Versteyhe wrote:
Dear all,
I would like to map (e.g. with Bowtie) collapsed sequences (tags) instead of individual sequence reads. Does anyone know if this is possible in Galaxy?
Thank you in advance.
Best regards,
*Soetkin Versteyhe, PhD** *PostDoc**
University of Copenhagen *Faculty of Health Sciences
*The Novo Nordisk Foundation* *Center for Basic Metabolic Research*
Integrative Physiology
Blegdamsvej 3B * *2200 København N
Denmark* ** *PHONE +45 35337116*
*_soetkin.versteyhe@sund.ku.dk__ _http://sund.ku.dk http://metabol.ku.dk http://metabol.ku.dk/* **
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