Deleted:Given a GTF or BED file of transcripts, get transcript types

Question

[Ethan]

Hello,

I have a GTF file of transcript types. I want to find the transcript types of the transcripts listed (lncRNA, protein coding, etc.).

My usual method of finding transcript types is to query Ensembl Biomart. However, I hate doing that, since it takes forever, requires manipulating the data into Ensembl's preferred formats, and is heavily dependent upon the servers and my internet connection being stable.

Is there a better method of querying for transcript types? I recently tried downloading the entire transcriptome in BED format from Ensembl, then using bedtools intersect to find exact matches, but I'm not too sure how accurate, precise, or limited my results would be.

I would greatly appreciate your help.