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Old 07-28-2010, 12:50 AM   #1
natstreet
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Default file format headaches - producing interleaved fastq

Hi

I have a load of paired end solid data as .csfasta and .qual files. I need to produce an interleaved fastq file from these for input into e.g. BFAST. Ideally I would also like to be able to produce a fastq file per read for properly paired mates and a third file of orphaned (single end) reads for use with e.g. Bowtie.

Can anyone point me to an existing script to do this or will I need to write one? I have looked at some existing options e.g. the Galaxy python solid2fastq script but so far I haven't managed to get it to output anything more than zero byte files. It also doesn't output the orphaned reads and re-scales everything to phred33, which is not always desirable.

I need to do the same for Illumina data as well, so if there is an option that also handles Illumina data (or is specific to it), that would be great.
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Old 07-28-2010, 02:04 AM   #2
natstreet
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Default Galaxy solid2fastq.py

I figured out why I was getting zero byte outputs from the Galaxy python script. It seems that for paired end input you HAVE to specify '-t true' because otherwise the name matching fails for every read. Obvious after some staring at the code but not otherwise.

So, now I still need to output the orphaned reads and a method to do the same for Illumina data.
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