FASTA to pseudo-FASTQ file?

[terencetate]

I am using the Galaxy server to process a FASTQ file from an Illumina run.

Having groomed to Sanger FASTQ, I am having a problem running FASTx barcode splitter and adaptor clipper tools, as these seemingly will only run on a FASTA file. Collapsing to FASTA sacrifices the quality scores, and will not run with the Galaxy BWA and Bowtie mapping implementations.

Can anybody suggest a means to convert a FASTA file back to a FASTQ file using arbitrary "perfect" Sanger quality scores?

Thanks.

[gaffa]

Hmm, I am pretty sure those FASTX utilities should be able to process FASTQ files. I presume the naming rationale in the FASTX package is that tools ending with "X" should handle both FASTA and FASTQ. I just tested fastx_clipper (v 0.0.13) on my machine and it seems to work fine. Do you get any kind of error message or something?

[terencetate]

I agree - they do, but the Galaxy implementation does not recognise FASTQ for some reason. I'm limited to Galaxy at the moment for this analysis...

[maubp]

Which Galaxy instance are you using? Have you checked with the administrators if it is the latest one? Certainly it looks like the one at usegalaxy.org supports FASTQ.

[terencetate]

http://main.g2.bx.psu.edu/

For the FASTx tool "Clip adapter sequence", I can only select FASTA files within my history, no FASTQ...

I'll get on to their support to see what the issue might be. Any suggestions for other FASTQ manipulation suites would be good - FASTX can't be the only option, right?

Thanks.

[maubp]

I use Biopython personally. If you want a scripting language supporting FASTQ other options include BioPerl, BioRuby and there is also BioJava.

For another command line tool suite with FASTQ support, try EMBOSS.