C. elegans CB4856 GTF/GFF file

Anusha_Aggarwal · 2024-08-21T14:39:03.855Z

Hi everyone!

Does anyone know where I can get access to a GTF/GFF file specific to the CB4856 C. elegans strain?

The GTF file posted on WormBase is empty, and the GFF file seems to have very limited & duplicated information (Index of /releases/WS293/species/c_elegans/PRJNA275000).

Please let me know, I would greatly appreciate any help!

HillelSchwartz · 2024-08-23T17:20:32.856Z

Have you tried to use the GBFF file at the NCBI, from this January?

Anusha_Aggarwal · 2024-08-23T17:38:30.559Z

I did check this file (GCA_963921145.1_CB4856_genomic.gbff.gz), but it doesn’t seem to have gene annotations. It seems to have genomic sequences and some other assembly information. Let me know if I might have overlooked something!

lybCNU · 2024-08-28T13:01:26.067Z

You can generate the gtf file yourself from the GFF3 file with tools such as agat_convert_sp_gff2gtf.pl from AGAT or GffRead .
Both tools can be installed easily by conda.