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Old 09-20-2015, 05:49 PM   #1
wisense
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Location: Shanghai,China

Join Date: Sep 2011
Posts: 30
Post How to clean the GTF file downloaded from Ensembl

Hi, all

Recently, I have downloaded a GTF file from Ensembl and found that there're coding and non-coding transcript annotations in the file. I just want to focus on the coding annotations, so can anyone tell me how to clean the GTF file?

The problem is that there're many types of transcripts in the GTF. Here's the list of each type:
Code:
antisense
IG_C_pseudogene
IG_J_pseudogene
IG_pseudogene
IG_V_pseudogene
lincRNA
miRNA
misc_RNA
Mt_rRNA
Mt_tRNA
nonsense_mediated_decay
non_stop_decay
polymorphic_pseudogene
processed_pseudogene
processed_transcript
protein_coding
pseudogene
retained_intron
rRNA
sense_intronic
sense_overlapping
snoRNA
snRNA
transcribed_unprocessed_pseudogene
unprocessed_pseudogene
I want to know which is coding and which is non-coding transcript.

Hope receive useful reply form you,

Thanks
wisense
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ensemble gtf, gtf annotation file, rna seq

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