gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] [-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end>] [-CTVNMAFGRUVBHSZWTOE] [-w <spl_exons.fa>] [-x <spl_cds.fa>] [-y <tr_cds.fa>] [-i <maxintron>] Filters ...
+ The -w flag outputs transcript sequences with spliced exons. + """ input: bio/gffread/wrapper.py (1) 37-40: Enhance the error message for fasta output flags While the validation is correct, the error message could be more informative by explaining what each flag produces: - "For fasta...
I have a transcript assembly gtf file (filename.gtf) generated by StringTie. To find the number of assembled sequences, I used the command: cut -f9 filename.gtf | cut -d ' ' -f4 | uniq | sort -u | wc -l This gives me 85371. Now I want to...
cuffgffread(input,output) reads the input GFF or GTF file and writes the mandatory columns to the output GFF file [1]. The function can also return the GTF-format file using the 'GTFOutput' option. cuffgffread requires the Cufflinks Support Package for the Bioinformatics Toolbox™. If the...