How to retrieve the transcript from gff file with the longest isoform? I tried using R , Biophython and other software also in ubuntu, but got so many installation problems.
If you anyone could help in solving this, it will be helpful.
The R script as follows,
proteome <- biomartr::getProteome(db = "refseq", organism = "Arabidopsis thaliana") annotation <- biomartr::getGFF(db = "refseq", organism = "Arabidopsis thaliana") # retrieve longest isoforms and store in new file retrieve_longest_isoforms(proteome_file = proteome, annotation_file = annotation, new_file = "Athaliana_pep_longest.fa") # import new file into R session Athaliana_pep_longest <- Biostrings::readAAStringSet("Athaliana_pep_longest.fa")
Thanks in advance. Aneesha