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GTF.awk
v1
0

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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
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  • gawk:4.1:d2acb41e

    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