transcript_to_gene_map: Create file associating transcript ids with gene ids

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

Description

Given a GTF file with both gene ids and transcript ids, write a csv with gene ids in the first column and transcript ids in the second.

Usage

transcript_to_gene_map(inFile, outFile)

Arguments

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

Details

Note that gene ids (in the first column of the output file) will be repeated when associated with multiple transcript ids. TIME: A minute or two.

Value

gene_transcript

Author(s)

Emma Myers

Examples

ids = transcript_to_gene_map("/Volumes/CodingClub1/RNAseq/Metadata/mm10_refGene.gtf", "/Volumes/CodingClub1/RNAseq/Metadata/RefSeq_id_map.csv")

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