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 KĂžbenhavn N

Denmark*
**
*PHONE +45 35337116*

*_soetkin.verste...@sund.ku.dk__
_http://sund.ku.dk
http://metabol.ku.dk <http://metabol.ku.dk/>*
**

*



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