Functional annotation, Illumina and PacBio transcript models

Functional annotation of merged structural annotations from short-read and long-read pipelines and six tissues.Structural annotations (transcript models) were merged with the TAMA tool tama_merge.py, fasta sequences extracted with Bedtools, protein-coding potential inferred with CPC2, open reading frames (ORFs) predicted and translated into amino acid sequences with the TAMA tool tama_orf_seeker.py, putative protein-coding sequences identified in the UniProt/UniRef50 database using blastp, results filtered and final annotation built with the TAMA tools tama_orf_blastp_parser.py and tama_cds_regions_bed_add.py, respectively.tama_merge.py options: ${-a 100 -z 100 -d merge_dup -f filelist.txt}filelist.txt settings, short-reads: "no_cap 2,1,2"filelist.txt settings, long-reads: "capped 1,2,1"bedtools options: ${getfasta -name -split -s}blastp options: ${-evalue 1e-10}