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Old 07-17-2014, 09:36 PM   #1
greenpuppy
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Default Help with the "secret" in EMBOSS for converting fast format from illumina to sanger

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
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Old 07-18-2014, 01:51 AM   #2
hpm
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Something like:

Quote:
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.
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Old 07-18-2014, 01:52 AM   #3
dpryan
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Just write a little bash script with a for loop.
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Old 07-18-2014, 01:53 AM   #4
dpryan
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@hpm: That will merge all of the files together, which greenpuppy mentioned not wanting.
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Old 07-18-2014, 10:42 AM   #5
greenpuppy
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I figured it out.

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