transcript_to_gene_fix: Replace transcript ids with gene ids in GTF file

In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description

Given a GTF file with transcript ids in the "gene_id" field and a file mapping these to gene ids, write a new GTF with gene ids in that field.

Usage

transcript_to_gene_fix(gtf, mapFile, outSuffix = "_geneids")

Arguments

gtf	String - Name of GTF with transcript ids in gene_id field
mapFile	String - Name of csv with gene ids in the first column and transcript ids in the second

Details

Use the transcript_to_gene_map function to create the mapFile input. TIME: Most of it's the "Replacing transcript ids with gene ids in key-value field" part, which is anywhere from 15-30m.

Author(s)

Emma Myers

Examples

transcript_to_gene_fix("/Volumes/CodingClub1/RNAseq/Metadata/mm10_refSeq_introns.gtf", "/Volumes/CodingClub1/RNAseq/Metadata/RefSeq_id_map.csv")

e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.