README.md

In yangjl/findpos:

findpos

INSTALLATION

INSTALL BLAST

First of all, find the lastest verion of BLAST from following ftp.

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

Download the appropriate version for your system. And then install it following here.

INSTALL R packages

### biostrings
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")

### install devtools
install.packages("devtools")

### install packages in development 
devtools::install_github("yangjl/findpos")

USAGE

The usage information can be found by typing ?findpos, which is the major function for this task. To run it, first of all, set up a blast database, i.e. example/16SMicrobialDB/16SMicrobial. And then specify the code for BLAST program, i.e. ~/bin/ncbi-blast-2.4.0+/bin. Note, the sequences of interest should be fasta format, i.e. example/rna.fasta. Finally, specify your mapping parameters, such as percent identity (iden) and mapped seq length (len). And then you just click and run.

library("Biostrings")
library("findpos")
### Find the help document for the function
?findpos

### run
res <- findpos(blastbin = "~/bin/ncbi-blast-2.4.0+/bin", db="example/16SMicrobialDB/16SMicrobial", fa="example/rna.fasta", iden=95, len=100)

yangjl/findpos documentation built on May 4, 2019, 2:28 p.m.