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Question: How to run a CDHIT command of "BioSeqClass" package on DNAStringSet object of DNA sequences to get non-redundent set of sequences?
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gravatar for vinod.acear
4 months ago by
vinod.acear20
India
vinod.acear20 wrote:

I am trying to run CDHIT , on DNAStringSet object of DNA sequences to get non-redundent set of sequences

library(Biostrings)

library("BioSeqClass")

## flank is DNAStrinSet object of equal length sequences

seq = as.character(flank)  
## Homolog reduction of whole-length sequence by cd-hit need cd-hit program;

I have downloaded latest CD-HIT programme and named its fiolder as "cd-hit" from the given link http://www.bioinformatics.org/download/cd-hit/  and given path of the given folder to cdhit.path in above command.

> reducSeq50 = hr(seq, method="cdhit", identity=0.5, cdhit.path="cd-hit")
Error in cdhitHR(seq, identity, cdhit.path) :
  cdhit.path cd-hit is not corrected

Please let me know where I am wrong.

 

 

 

 

 

ADD COMMENTlink modified 3 months ago • written 4 months ago by vinod.acear20
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