Hi Bioconductors,
I have a question regarding to GTF/GFF3's start and end positions in the
genome and I dont know if here is the right place to ask. I would be
appreciated if anyone can answer my question.

Does anybody know the numbers regarding to start position and end positions
in GTF/GFF3 files are based on which version of reference genome? I see
different versions: hard_masked.fa or soft-masked.fa, cds.fa,
cds_primaryTranscriptOnly.fa. I have a GTF file and I want to find the
corresponding sequences in the fasta references, but I dont know which file
to use. I used the hardmasked one in which we used to map the reads to
genome, but corresponding positions in the GTF file does not give me
correct sequence for the each gene.


Sincerely Yours,
Delasa Aghamirzaie
Genetics, Bioinformatics, and Computational Biology (GBCB) PhD Student
Virginia Tech
Blacksburg, Virginia

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