The First Korean Stroke Genetics Association Research (The FirstKSGAR) Consortium

Hi all,

Forgive me if this question has been posted before (I'm new to this forum). In the past, when doing transcript-level RNA-seq analyses, I have used the gffread utility to pull transcript sequences for annotation and downstream functional analyses.

i.e. gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

However, I am currently working on a gene-level analysis and am having issues doing something similar - especially in regard to evaluating novel loci in my Stringtie assemblies. The way I see it, I have one of two options:

1) Use my RefSeq IDs for non-novel loci and annotate novel loci separately and then merge these annotation lists prior to functional analysis. (If I go this route, I still need to generate a FASTA with the novel loci anyway)

or

2) Pull all gene/loci sequences and re-annotate everything

Is there a (relatively) simple work-around for this?