WebAll groups and messages ... ... WebTopHat[36] v1.2.3 and also Cufflinks[37] v0.Being unfaithful.3 were utilized to be able to line-up and method these kind of quick scans. Your script tophat2gff3 and cufflinks2gff3 have been after that utilized to procedure the final results into GFF3 file format.

[maker-devel] Non-unique top level ID - Google Groups

WebYou should be using maker2eval_gtf. The scripts you mention were actually deprecated in MAKER 2.10 onwards (about 5 years ago). You may be looking at old documentation. WebDec 22, 2011 · The script tophat2gff3 and cufflinks2gff3 were then used to process the results into GFF3 format. The resulting GFF3 files were provided to the est_gff option in … fish in baltimore harbor

VCRU Bioinformatics - Install notes

TopHat and Cufflinks generally expect exon features to define a transcript structure, with optional CDS features to specify the coding segments. Our GFF reader will ignore redundant features like start_codon, stop_codon when whole CDS features were provided, or *UTR features when whole exon features were also given. http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/2012-October/003884.html Webcufflinks2gff3 transcriptome_models.gtf > transcriptome_models.gff3 Optimized procedure for mining SSP genes from genomic sequences using the MAKER pipeline MAKER is a portable and easily configurable genome annotation pipeline. This pipeline is pre-installed and available in Docker image. It can be freely downloaded under the GNU license. fish in az