Combines GENCODE40 and lncipedia5.2 gene annotations in a non-redundant manner.

Can be run with the following command:

bash generateAnnotation.sh

Dependencies:

• gffread

R packages:

• rtracklayer
• tidyverse
• VennDiagram

Note 1: gtf can be converted to bed with ucsc tools http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

gtfToGenePred -genePredExt -geneNameAsName2 gencode_v40.lncipedia_v5_2_hc.annotation.gtf gene.tmp
genePredToBed gene.tmp gencode_v40.lncipedia_v5_2_hc.annotation.bed12

Note 2: salmon index can be created like so

salmon index -t gentrome.fa.gz -d decoys.txt -p 20 --gencode -i salmon_index/