Additional scripts

Additional Perl scripts for the tufted duck annotation project and R scripts for visualisation of results.Perl scripts:tama_merge_report_parser.pl: parse gene report of tama_merge.pytblout2gff3.pl: convert cmscan's toblout result to gff3 formatR scripts:ncRNA_distributions.R: exons per transcript and transcript length distributionsprotein_coding_potential.R: Venn diagram for CPC2-predicted and UniRef50 identified ORFstranscript_model_histograms.R: histograms for structural annotations per tissue and pipelineUpSetR_uniprot_supported.R: evidence for expressed genes per tissue/pipelineInput files:all_counts_hisat_stringtie_threshold_ends.txt: count data for transcript_model_histograms.Rexons_per_transcripts.txt and transcript_lengths.txt: count data for ncRNA_distributions.Rgene_report_supported_by_uniprot.csv: binary TRUE or FALSE for gene report by tissue/pipeline; input for UpSetR_uniprot_supported.Rgenes_found_cpc.txt and genes_found_uniprot.txt: identified genes CPC2 and UniRef50; input for protein_coding_potential.R