SOLiD csfasta to fastq using BFAST+BWA

[flobpf]

Hi,

I'm trying to convert my SOLiD reads to FASTQ using BFAST+BWA's solid2fastq.pl utility. I have two sets of paired-end files

*_F3.csfasta
*_F3_QV.qual
*_F5-DNA.csfasta
*_F5-DNA.QV.qual

However, the solid2fastq.pl utility only allows files labeled F3 and R3

Note: <in.title> is the string showed in the `# Title:' line of a
".csfasta" read file. Then <in.title>F3.csfasta is read sequence
file and <in.title>F3_QV.qual is the quality file. If
<in.title>R3.csfasta is present, this script assumes reads are
paired; otherwise reads will be regarded as single-end.

The read name will be <out.prefix>: panel_x_y/[12] with `1' for R3
tag and `2' for F3. Usually you may want to use short <out.prefix>
to save diskspace. Long <out.prefix> also causes troubles to maq.

The SOLiD documentation (see here), however, says that F5 is for paired end and R3 is for mate-pair. My reads are paired end and so they are labeled F5.

My question is how do you go about merging these two files? Is it as simple as renaming the F5-DNA files as R3? I also notice in the documentation that F5 and R3 are in opposite orientation. Is it then required to reverse-complement the F5 reads to make them R3? How is that done? Am I missing something?

If solid2fastq cannot accomplish this task, do you know of any other programs which could do this? Finally, I want to:
1) Trim adapters from each paired-end file individually using cutadapt (which takes a FASTQ file)
2) Map the filtered reads using BFAST (which also takes a FASTQ file)

Thanks

[jparsons]

Cutadapt accepts csfasta and qual input. It will even output a fastq afterwards.
http://seqanswers.com/forums/showthread.php?t=7100 should take it from there.