gffread conversion leaves gene_id

Question

[piyushjo]

Hi,

I am trying to get a gtf from gff. I used the following code format

gffread example.gff -T -o example.gtf

The output contains chromosome information but leaves out gene_id information and just keeps transcript_id information. I wish to know how can I keep both information in the output .gtf. The .gff files contains the information for both the aspects, so missing values is not the case.

Answer 1

[piyushjo]

I think I solved it. gffread example.gff -F -T -o example.gtf

[Kevin Blighe]

Can you confirm 100%?

[piyushjo]

Yes it worked. Before when I generated gtf without -F option the output file only had transcript id in description. With -F option it contains all the information as found in the original .gff.

ex:

chr1    lncipedia.org   exon    30564   30667   .   +   .   transcript_id "MIR1302-2HG:2"; gene_id "MIR1302-2HG"; transcript_id "MIR1302-2HG:2"; gene_alias_1 "ENSG00000243485.1"; gene_alias_2 "MIR1302-10"; gene_alias_3 "OTTHUMG00000000959.2"; gene_alias_4 "ENSG00000243485.2"; gene_alias_5 "ENSG00000243485.3"; gene_alias_6 "RP11-34P13.3"; gene_alias_7 "ENSG00000243485.4"; gene_alias_8 "MIR1302-2"; gene_alias_9 "ENSG00000243485.5"; gene_alias_10 "MIR1302-2HG"; transcript_alias_1 "ENST00000473358.1"; transcript_alias_2 "MIR1302-10-001"; transcript_alias_3 "OTTHUMT00000002840.1"; transcript_alias_4 "NONHSAT000011";

I hope it works for others too and they can further confirm it.

[Kevin Blighe]

Great - thank you for coming back to confirm. This will help others searching for the same issue via a search engine.