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.
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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