Variant Analysis of PacBio Reads
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:
- Map these reads to my original gene of interest,
- Then filter reads based on an identity score,
- 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.
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pthom010 •
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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.
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.