runPRAM: Predict intergenic transcript models from RNA-seq

In pliu55/pram: Pooling RNA-seq datasets for assembling transcript models

Predict intergenic transcript models from RNA-seq

Description

Predict intergenic transcript models from RNA-seq

Usage

runPRAM(in_gtf, in_bamv, out_gtf, method, cufflinks = "",
    stringtie = "", taco = "")

Arguments

in_gtf	An input GTF file for defining genomic coordinates of existing genes. Required to have 'gene_id' in the attribute column (column 9)
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'
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: ”

Value

None

Examples

in_gtf = system.file('extdata/demo/in.gtf', package='pram')

in_bamv = c(system.file('extdata/demo/SZP.bam', package='pram'),
            system.file('extdata/demo/TLC.bam', package='pram') )

pred_out_gtf = tempfile(fileext='.gtf')

## assuming the stringtie binary is in folder /usr/local/stringtie-1.3.3/
## you can run runPRAM() by the following example
##
# runPRAM(in_gtf, in_bamv, pred_out_gtf, method='plst',
#         stringtie='/usr/local/stringtie-1.3.3/stringtie')

pliu55/pram documentation built on March 30, 2024, 7:24 p.m.