Methods to convert SOLiD reads to nucleotide space

Question

[gsc529]

Hello,

I would like to know if there are any methods that can be used to convert colorspace reads from BAM files generated from colorspace reads on the SOLiD system to nucleotide space?

I am looking to use analyze some data generated a number of years ago using both SOLiD 3 and SOLiD 4 systems for alternative splicing. I currently have the aligned BAM files that were generated using LifeScope software but I do not, however, have the csfastq's. I am hoping to run the data through rMATS, or a similar package, to look at alternative splicing events in two different study groups (case vs control). Are there any such things similar to rMATS that would be better suited to handle colorspace?

Any suggestions/guidance would be greatly appreciated! Thank you

[Ram]

Titles should be brief and clear. Titles convey what the post is about and should not contain text that goes in the body of the post. In your case, "Methods to convert SOLiD reads to nucleotide space" would have been a much better title than this wall of text.

Answer 1

[colindaven]

Because the reads were aligned against a reference, you can just use BAM 2 fastq methods to extract the sequences. That way you get a FASTQ and avoid colourspace altogether, which I would not recommend using for RNA-seq projects in any case.

You can use a modern samtools for this:

samtools fastq

No input file specified.
Usage: samtools fastq [options...] <in.bam>
Options:

[GenoMax]

Do you know if this works with SOLiD data and generate correct results?

In this day and age there is really no good reason to work with colorspace data. OP should ideally find a new/more current dataset.

[colindaven]

Yep, it works, yep, they should use other data - but that wasn't the question.

I'd probably trust it for alignments, but not for SNV calls as you're not using the colour space information.