file format headaches - producing interleaved fastq

natstreet · 07-28-2010, 12:50 AM

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.

natstreet · 07-28-2010, 02:04 AM

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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07-28-2010, 12:50 AM	#1
natstreet Member Location: Sweden Join Date: Nov 2009 Posts: 83	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.

07-28-2010, 02:04 AM	#2
natstreet Member Location: Sweden Join Date: Nov 2009 Posts: 83	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.