Align sequences without quality data

[KDK]

Hi

I have a file with ~32,000 short DNA sequences (120 base pairs). I'd like to align this to the genome and generate a track for UCSC. Alignment programs I have used previously all require fastq files, and I do not have quality data. All I have is a text file with a sequence on each line. Is there another option in Galaxy, or another database that will work for this alignment?

Thank you very much

Kristin

[mastal]

I don't know what is available on Galaxy, but Bowtie will take fasta files as input.

[KDK]

Thanks, I looked at this, the problem is I don't have it in fasta format either. I just have a list of sequences and am not sure how to get an interspersed <with an indentifier for each?

Basically I was given a list of sequences as an output for probes for a selection RNA-seq experiment. The company gives it to you in this format and says to trust them things are designed properly but I would really like to check myself.

[mastal]

Have a look at the bowtie manual, under the heading 'Input'

http://bowtie-bio.sourceforge.net/manual.shtml#input

Apparently it also takes what it calls 'raw data', one sequence per line,
which sounds like what you have.

[KDK]

Awesome, thank you so much for your help!