salmon_par: quantify transcript levels using 'pseudo-alignments'

In pcahan1/CellNet: Assess and improve cell fate engineering with network biology

quantify transcript levels using 'pseudo-alignments'

Description

Uses salmon

Usage

salmon_par(sampTab, sname = "sra_id",
  salmonIndex = "/media/ephemeral1/dat/ref/MM_GRCh38.SalmonIndex.030816",
  cname = "trimNames", libraryType = "U", numThreads = 5,
  destPrefix = "salmonRes", njobs = 4,
  salmonPath = "~/rnaseq/SalmonBeta-0.6.1_DebianSqueeze/bin")

Arguments

sampTab	sample table
sname	colname to id sample
salmonIndex	salmon index directory
cname	trimNames
libraryType	library type (unstranded, etc)
numThreads	number of threads to use
destPrefix	where should the resulting files be placed
njobs	use shell parallel too, and allot njobs
salmonPath	path to salmon binary

Value

vector of output names

pcahan1/CellNet documentation built on May 18, 2023, 4:58 p.m.