Question: Variant Analysis of PacBio Reads
0
gravatar for pthom010
17 months ago by
pthom0100
pthom0100 wrote:

I have several multifasta files that contain PacBio reads of a gene of interest. I have one file of multifastas for several genotypes of a particular species. I would like to do a variant analysis on these reads but don't know where to start. Would it be possible to do the following:

  1. Map these reads to my original gene of interest,
  2. Then filter reads based on an identity score,
  3. Then take my filtered reads and do a variant analysis calling out SNPs or other polymorphisms between genotypes?

A GUI would be nice, but I expect to do this in R so any R-programs would be greatly appreciated. Thanks.

sequencing R • 469 views
ADD COMMENTlink written 17 months ago by pthom0100

multifasta files that contain PacBio reads

Do you know if these were generated by CCS or are they individual subreads converted to fasta format? If latter they may have a significant amount of error in them.

ADD REPLYlink written 17 months ago by genomax74k

Unfortunately I believe it was the latter. The reads were multiplexed with two other experiments (beyond my control) and I'm left with several multifastas containing as manny as 300 reads.

ADD REPLYlink written 17 months ago by pthom0100
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