fasta to fastq

[luana]

Hello guys

I' m working with TopHat and Bowtie to start my Phaseolus' RNAseq analysis, but to use this protocol I need to convert the cDNA sequences .fasta to .fastq.

What software can I use?

[GenoMax]

Normally one would start with NGS data already in fastq format when doing Tophat analysis.

If you want to convert your fasta sequences to fake fastq then you could use reformat.sh from BBMap like so

$ reformat.sh in=test.fa out=fake.fq qfake=35

[SES]

I would recommend not doing this reformatting approach, or at least proceeding with caution. With FASTA, you can be certain that the quality scores won't be used, but with a fake FASTQ you may be introducing artifacts. That is, unless you can be certain that the quality scores won't be used, but I'm not sure you can force this behavior with these tools.

For a tool that just needs the sequences there is obviously no harm in going to FASTQ so a parser will work. For an aligner, I'd be cautious since they use quality scores.