Using Fasta Sequence Reads In Galaxy

Question

[Paul]

Hi, I'm wondering if anybody has any experience of trying to process fasta sequence reads using Galaxy? Galaxy doesn't seem to accept fasta reads by default.

I guess you'd have to convert to fastq locally first (there doesn't seem to be a tool for that on Galaxy), which would probably involve leaving the quality score column blank, which might cause problems downstream I guess.

Just wondering if anyone has tried this. If Galaxy can't handle fasta it looks like I can use Bowtie to align them locally.

[ALchEmiXt]

So you want to use a short-read mapper Bowtie to do what? Where did your data originate from? From a NGS sequencing project? If so try to use quality retaining formats like fastq or fasta+qual.

[Paul]

There data is from this paper "http://www.biomedcentral.com/1471-2164/10/161" and is available here "http://www.picb.ac.cn/Comparative/data.html". Unfortunately the data is only available in fasta format. I'd like to use Bowtie (or any other suitable aligner) map the data and cufflinks (or some suitable equivalent) to assess gene expression for these samples.

Answer 1

[Casey Bergman]

I don't know why you say galaxy can't use fasta. Fasta is a default data type under "get data"->"upload data"

Also Galaxy does have a fasta+qual -> fastq converter under NGS: QC and manipulation -> Roche-454 data -> Combine FASTA and QUAL into FASTQ.

[Neilfws]

My understanding is that Galaxy can do "most" things, given the appropriate wrapper.

[ALchEmiXt]

+1 And it is under 454 since one of the formats coming from 454 in addition to the default sff is the fasta+quality.

[ALchEmiXt]

+1 And it is under 454 since one of the formats coming from 454 in addition to the default sff is the fasta+quality! There are also FASTA to tabular conversion tools for all kind of post-processing stats (as used in for instance metagenomics->BLAST->filters->TAXID->and so forth).

Answer 2

[Damian Kao]

Not sure how up to date this is, but here is a solution.

[Paul]

Ah excellent "Roche-454 data" seems an odd place for this tool though!?