How to convert multiple .fa file to .fastq in Shell

Question

[nhatphamduy2000]

Hello everyone,

I know how to convert 1 .fa to .fastq but not many as a time in Shell

perl fasta_to_fastq.pl reads.fasta > my_converted_fasta.fq

please help me with this! Thank you very much!

[Prasad]

use faToFastq utility and loop through your fasta files

Answer 1

[Brian Bushnell]

Using BBMap:

cat *.fasta | reformat.sh in=stdin.fa out=x.fq

There are few situations where this would be useful.

Answer 2

[WouterDeCoster]

Assuming that script is valid you can probably just do a loop over the input files, e.g.:

for f in *.fasta ; do perl fasta_to_fastq.pl $f > $f.conv.fq ; done