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Old 10-13-2015, 09:24 PM   #1
huan
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Post Any Tools/Workflows For PacBio IsoSeq SSR Analysis?

We have used the SMRT(Pacific Biosciences) sequencing system PacBio RS II to generate cDNA sequences. After isoform-level clustering, polishing and trimming of raw data, non-redundant contigs were obtained. Next we want to do the Fragment analysis( microsatellite or SSR/STR), So is there any tools or workflow now available for the microsatellite or SSR/STR analysis?

Thanks a lot for any apply
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Old 10-20-2015, 10:48 AM   #2
Magdoll
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Hi,

I don't have personal experience with microsatellites however there seems to be some existing tools for it.

Theoretically, it should not be hard to apply most tools developed for ESTs or genomes to PacBio Iso-Seq (cDNA) data.

Two relevant papers:

http://bioinformatics.oxfordjournals.../10/1181.short

http://genome.cshlp.org/content/10/7...e2=tf_ipsecsha

For longer alpha satellite, there is a recent paper by PacBio's Jason Chin and collaborators.

https://github.com/volkansevim/alpha...ster/README.md
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