SOLiD to NCBI SRA

[Chandana]

Hi,
Can anyone help me to convert SOLiD data in .qual and .csfasta format into the FASTQ format used by NCBI SRA? Similaly, is there a way to separate a color space FASTQ in NCBI SRA into corresponding .qual and .csfasta files?

[twaddlac]

There are some scripts in the bfast and bwa packages as well as many of the other colorspace compatible software packages. Alternatively I'm sure that Galaxy has something that can help solve your problem.

I hope this helps!

[Chandana]

Thanks a lot twaddlac, I have solved my problem using the SRA toolkit.
For splitting SRA fastq to .qual and .csfasta I used the abi-dump tool in SRA toolkit. The script solid2fastq.pl in BWA fails to run on these files, so I had to modify it, Basically I changed the regular expression used to identify the description of reads to match the one produced by the SRA toolkit.