Hello,

Yes, you can generate a FASTQ file with dummy quality scores from a FASTA file. Use the Combine FASTA and QUAL into FASTQ tool under NGS: QC and manipulation-->ROCHE-454 DATA. For the Quality Score File, leave it set with the default option ("Selection is Optional"). The quality value will be ~ for each base

Regards,

Kelly

On Sep 17, 2010, at 4:10 PM, Ada Sedova wrote:

Dear galaxy,

I have some sequence data that is in fasta format, and I would really like to run bowtie on it for mapping. The bowtie article claims that bowtie can map with fasta files, but galaxy does not allow it. Is there anything I can do to fix this? For instance, is there a way to add some kind of q values to the file so it will run? 

Thanks

_______________________________________________
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-user