[mmartin]

Thanks for your answer! We'll report back if we manage to get it to work.

As for your question (maybe this should be moved to a new thread): An example for a splice alignment is in the SAM paper (The Sequence Alignment/Map Format (SAM) and SAMtools by Li et al, 2009), Figure 1, read r004. The alignment for that read contains an 'N' operation in the CIGAR string ("Skipped region from the reference").

That seems to work only if both parts of the read map to the same contig, in the correct order and on the same strand.

[lix]

Hi adameur,

Do the SplitSeek and the AB WT analysis pipeline support the paired-end SOLiD data?


lix

[adameur]

Hi lix,

That's an interesting point. I have not yet tried SplitSeek for paired-ends but I think it could be useful, both to detect junctions in the gap between the paired-ends and inside the reads.

What you could try is to do a mapping and pairing, extract all read pairs separated by a distance greater than the fragment length into a BEDPE formatted file, and then run splitseek.pl. That should give you junctions located between the two ends. Next, you could extract all 50bp reads that were not mapped at full length and do a normal SplitSeek run for those (including a split read mapping).

[krobison]

TopHat now supports colorspace, though I have not yet actually succeeded with using it.

See this thread; in particular, make sure you install the patches.

[Calle]

Bedtools converts sam --> various bed formats (http://code.google.com/p/bedtools/)

Hi mmartin,

The AB WT pipeline performs a split read mapping where the two ends of the read are independently aligned to the reference. This type of split read alignment is essential if you want to run SplitSeek, otherwise you risk missing a lot of junctions. As far as I know there are currently no good alternatives to the WT pipeline for running SplitSeek.

About converting the SAM/BAM to BEDPE. I suppose this could be done quite easily. For me, the main concern is whether or not most split read alignments are included in the SAM/BAM alignment results. And that will depend on which mapping algorithm was used.

By the way, does anyone know how a split read alignment is represented in SAM?

/Adam