Gathering Data for CLIP_Analysis

To get GTF files follow the instructions on the genome browser for generating GTF files. Alternatively you can make your own as long as they have 5UTR, 3UTR, exon and CDS definitions. Clipper will infer intron positions to generate graphs for distal and proximal introns

http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

Specifically run this command: genePredToGtf -utr hg19 knownGene knownGene.gtf to generate the required GTF file.