Truwl

BETA
gawk
Version: 4.1
Identifier: TL_9579db.89
TL_9579db.89.1C10
0
Overview
Create a combined GTF file from Gencode annotations, Gencode tRNAs, and spike-ins fasta usage: gawk -f GTF.awk genomeAnnotationGRF tRNAAnnotationGTF spikeInFasta > mergedGTF input files: genomeAnnotationGTF: main gtf file, e.g. "gencode.v19.annotation.gtf" tRNAAnnotationGTF: gtf file for tRNAs or other annotations - exons only! spikeInFasta: fasta file with spike-ins, e.g. "spikes.fixed.fasta" output file: MergedGTF: Single merged GTF file to be used for genome generation with STAR, RSEM, TopHat
Usage
Associations
Input Files
  • GTF.awk

    GTF.awk v1.0 creates GTF file from Gencode annotations, Gencode tRNAs, spike-ins fasta. usage: GTF.awk main.gtf tRNA.gtf spikein.fasta > combined.gtf

  • gencode.v25.annotation_chr22Entries.gtf

    Gencode genome annotation file filtered to only contain annotations for chromosome 22. Original whole file at https://www.gencodegenes.org/releases/25lift37.html

  • gencode.v25.tRNAs_chr22Entries.gtf

    Transcript Gencode annotation file. Filtered to only contain annotations for chromosome 22.

  • ENCFF001RTP.fasta

    Ambion spike-in concentrations and subgroups for mix 1 and mix 2

Output Files
  • mergedGTF.gtf

    GTF created by combining gencode annotations, gencode transcriptome annotations and spike-in fasta. File produced with GTF.awk.