Help with the "secret" in EMBOSS for converting fast format from illumina to sanger

[greenpuppy]

Hi,

I'm currently looking for tools to convert fastq file format from illumina 1.3 to sanger. I googled a little bit and found EMBOSS is capable of handling such tasks. I managed to convert the file format in a single fastq file with the following command:

seqret fastq-illumina::input.fastq fastq-sanger:utput.fastq

However, I failed to find a way to execute this on multiple fastq files at a time. My goal is to generate multiple output fastq files with each corresponding to a single input fastq file. I have about 50 files, and I don't want to write the command 50 times, with each time changing the filenames in the command.

Can anyone help me out? Thanks

Huan

[hpm]

Something like:

cat input*.fastq | seqret -filter -auto -sformat fastq-illumina -osformat fastq-sanger -out output.fastq

should do the trick.

Note: to avoid potential problems ensure your input file pattern will not include your output file.

See 'seqret -help -verbose' and the EMBOSS documentation (http://emboss.open-bio.org/ and http://emboss.sourceforge.net/) for more information.

[dpryan]

Just write a little bash script with a for loop.

[dpryan]

@hpm: That will merge all of the files together, which greenpuppy mentioned not wanting.

[greenpuppy]

I figured it out.

ls *fastq | xargs -I {} -P 12 seqret fastq-illumina::{} fastq-sanger::new_{}