Hi guys,
I have been trying to use gtf2bed to convert a gtf file to bed format, but to no avail. On running the following command -
gtf2bed < GRCh38p5_copy.gtf > foo1.bed
it gives the error -
Error: Potentially missing gene or transcript ID from GTF attributes (malformed GTF at line [1]?)
I checked the first few lines of the gtf (removed the commented lines too). They are-
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
Also, I tried to run the tool on the example gtf file mentioned on their own website but the output bed file it gives me is empty.
Any ideas what could be going wrong?
Hi Alex,
But as I mentioned in my question (the 2 lines I copied from the gtf), the
transcript_id
is present in the gtf.Also, what could be the reason that even the example gtf file provided in the website (foo.gtf) also generates an empty bed file?
Take another look at your sample file. Not sure what's up with the demo file (I'll look into it) but your sample input does not meet spec.