Application of PacBio based cDNA data in RNA-Seq analysis

[apratap]

Hi Everyone

Just wanted to know how people are using cDNA sequence data obtained from PacBio. Just curious to see and understand downstream applications in conjunction to Illumina cDNA data. Any relevant papers that you could point me to would help too.

PS : cross posted on biostar to get more visibility and hopefully responses


Thanks!
-Abhi

[maubp]

Where's the URL for the biostar cross post?

[apratap]

Hi maubp

hers the URL for biostar corss posting.

http://biostar.stackexchange.com/questions/17232/application-of-pacbio-based-cdna-data-in-rna-seq-analysis

-Abhi

[jnfass]

I'm having trouble finding bioinformatics protocols for doing this too. The problem seems to be that most tools (scripture, PASA?, IsoInfer, Inchworm, IsoEM, NSMAP, MISO are most of what I've looked at) seem to depend on spliced alignments produced by, e.g. Tophat. But the only tools that align PacBio reads well (PB's BLASR, and BWA's bwasw command) don't produce spliced alignments, as far as I can tell.

Let's add the terms isoform inference, alternative splicing, transcript, exon, splice junction, to improve search results for this thread.

[jbingham]

You might look at pacBioToCA and P_ErrorCorrection. They can be used to error correct PacBio reads using Illumina reads. Then the polished reads can be input to a wider variety of tools and you may be able to get spliced alignments.

[mchaisso]

I'm having trouble finding bioinformatics protocols for doing this too. The problem seems to be that most tools (scripture, PASA?, IsoInfer, Inchworm, IsoEM, NSMAP, MISO are most of what I've looked at) seem to depend on spliced alignments produced by, e.g. Tophat. But the only tools that align PacBio reads well (PB's BLASR, and BWA's bwasw command) don't produce spliced alignments, as far as I can tell.

Let's add the terms isoform inference, alternative splicing, transcript, exon, splice junction, to improve search results for this thread.

Hi, right now we're using GMAP to produce spliced alignments. It's a bit slow, but it is fairly sensitive for single pass raw pacbio reads (not ccs and not error corrected), and produces SAM output that is easily integrated into analysis pipelines. The only problem I've seen so far is some merging of exons.

I'd be happy to hear of any analysis of GMAP.

BLASR does not handle spliced alignment.

Should I cross post on biostar?