buildModel: Build transcript models from aligned RNA-seq data

In pram: Pooling RNA-seq datasets for assembling transcript models

Description

Build transcript models from aligned RNA-seq data

Usage

buildModel(in_bamv, out_gtf, method = "plcf", nthreads = 1,
    tmpdir = NULL, keep_tmpdir = FALSE, cufflinks = "",
    stringtie = "", taco = "", cufflinks_ref_fa = "")

Arguments

in_bamv	A character vector of input BAM file(s). If mode 'cf' or 'st' is used, only one input RNA-seq BAM file is allowed. Currently, PRAM only supports strand-specific paired-end data with the first mate on the right-most of transcript coordinate, i.e., 'fr-firststrand' by Cufflinks's definition.
out_gtf	An output GTF file of predicted transcript models
method	A character string defining PRAM's model building method. Current available methods are: plcf: pooling + cufflinks plst: pooling + stringtie cfmg: cufflinks + cuffmerge stmg: stringtie + merging cftc: cufflinks + taco cf: cufflinks st: stringtie Default: 'plcf'
nthreads	An integer defining the number of threads to-be-used. Default: 1
tmpdir	A character string defining the full name of a folder for saving temporary files. If not tmpdir is give, PRAM will use R's tempdir().
keep_tmpdir	Whether to keep temporary files afterwards. Default: False
cufflinks	Cufflinks executable. Required by mode 'plcf', 'cfmg', and 'cf'. For mode 'cfmg', executable files of Cuffmerge, Cuffcompare, and gtf_to_sam from the Cufflinks suite are assumed to be under the same folder as Cufflinks. All the executables are available to download for Linux http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz and MacOS http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz. Souce code can be obtained from http://cole-trapnell-lab.github.io/cufflinks/. Default: ”
stringtie	StringTie executable file. Required by mode 'plst', 'stmg', and 'st'. Executable can be downloaded for Linux http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.Linux_x86_64.tar.gz and MacOS http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.OSX_x86_64.tar.gz. Souce code can be obtained from https://ccb.jhu.edu/software/stringtie/. Default: ”
taco	TACO executable file. Required by mode 'cftc'. Executable can be downloaded for Linux https://github.com/tacorna/taco/releases/download/v0.7.0/taco-v0.7.0.Linux_x86_64.tar.gz and MacOS https://github.com/tacorna/taco/releases/download/v0.7.0/taco-v0.7.0.OSX_x86_64.tar.gz. Souce code can be obtained from https://tacorna.github.io. Default: ”
cufflinks_ref_fa	Genome reference fasta file for Cufflinks. If supplied, will be used for cufflinks's '–frag-bias-correct' and cuffmerge's '–ref-sequence' options. Default: ”

Value

None

Examples

fbams = c(  system.file('extdata/bam/CMPRep1.sortedByCoord.clean.bam',
                        package='pram'),
            system.file('extdata/bam/CMPRep2.sortedByCoord.clean.bam',
                        package='pram') )

foutgtf = tempfile(fileext='.gtf')

## assuming the stringtie binary is in folder /usr/local/stringtie-1.3.3/
## you can run buildModel() by the following example
##
# buildModel(fbams, foutgtf, method='plst', 
#            stringtie='/usr/local/stringtie-1.3.3/stringtie')

pram documentation built on Nov. 8, 2020, 11:08 p.m.