gtf file for canFam2 genome version

Question

[1769mkc]

I'm trying to find out gtf file for this version of the canine I looked both ncbi as well as ucsc. I am not able to find the gtf file.

Here when I try to download I don't see the option to download the gtf file

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002285.2/

Normally in ucsc there is a folder called genes as we see in case of hg19 https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/genes/ where it contains the gtf file but that is not present in canFam2 ucsc.

https://hgdownload.cse.ucsc.edu/goldenPath/canFam2/bigZips/

Is there a way which I can find already created gtf for the same version which is canFam2 either from ncbi or ucsc ?

It would be helpful to know if that is possible to download

[GenoMax]

Are you specifically looking for canFam2? Likely because newer versions available now: https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=9612

[1769mkc]

yes I'm looking for this canFam2 only that for some specific cases I have to use, even though I have the newer version also

Answer 1

[Pierre Lindenbaum]

I wrote https://jvarkit.readthedocs.io/en/latest/KgToGff/

It was just a one-shot, I don't have used it much. Please check the results.

$ wget -qO - "https://hgdownload.cse.ucsc.edu/goldenPath/canFam2/database/ensGene.txt.gz" | gunzip -c |\
  java -jar dist/jvarkit.jar kg2gff --gtf | head -n 20
chr29   ucsc    gene    31843577    31869014    .   +   .   ID "GENE2"; Name "ENSCAFG00000008510"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; gene_type "protein_coding";
chr29   ucsc    transcript  31843577    31869014    .   +   .   ID "ENSCAFT00000013501.3"; Parent "GENE2"; Name "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3"; transcript_name "ENSCAFT00000013501";
chr29   ucsc    exon    31843577    31843766    .   +   .   ID "ENSCAFT00000013501%3AE0"; Parent "ENSCAFT00000013501.3"; Name "ENSCAFT00000013501"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3"; exon_id "ENSCAFT00000013501%3AE0";
chr29   ucsc    exon    31862157    31862334    .   +   .   ID "ENSCAFT00000013501%3AE1"; Parent "ENSCAFT00000013501.3"; Name "ENSCAFT00000013501"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3"; exon_id "ENSCAFT00000013501%3AE1";
chr29   ucsc    exon    31865271    31865385    .   +   .   ID "ENSCAFT00000013501%3AE2"; Parent "ENSCAFT00000013501.3"; Name "ENSCAFT00000013501"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3"; exon_id "ENSCAFT00000013501%3AE2";
chr29   ucsc    exon    31868495    31868660    .   +   .   ID "ENSCAFT00000013501%3AE3"; Parent "ENSCAFT00000013501.3"; Name "ENSCAFT00000013501"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3"; exon_id "ENSCAFT00000013501%3AE3";
chr29   ucsc    exon    31868849    31869014    .   +   .   ID "ENSCAFT00000013501%3AE4"; Parent "ENSCAFT00000013501.3"; Name "ENSCAFT00000013501"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3"; exon_id "ENSCAFT00000013501%3AE4";
chr29   ucsc    CDS 31843577    31843766    .   +   0   ID "CDS4"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    CDS 31862157    31862334    .   +   2   ID "CDS5"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    CDS 31865271    31865385    .   +   1   ID "CDS6"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    CDS 31868495    31868660    .   +   0   ID "CDS7"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    CDS 31868849    31868910    .   +   2   ID "CDS8"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    three_prime_utr 31868911    31869014    .   +   .   ID "UTR9"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    start_codon 31843577    31843579    .   +   .   ID "codon10"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr29   ucsc    stop_codon  31868908    31868910    .   +   .   ID "codon11"; Parent "ENSCAFT00000013501.3"; biotype "protein_coding"; gene_id "GENE2"; gene_name "ENSCAFG00000008510"; transcript_id "ENSCAFT00000013501.3";
chr3    ucsc    gene    72230308    72416756    .   +   .   ID "GENE13"; Name "ENSCAFG00000015634"; biotype "protein_coding"; gene_id "GENE13"; gene_name "ENSCAFG00000015634"; gene_type "protein_coding";
chr3    ucsc    transcript  72230308    72416756    .   +   .   ID "ENSCAFT00000024802.14"; Parent "GENE13"; Name "ENSCAFT00000024802.14"; biotype "protein_coding"; gene_id "GENE13"; gene_name "ENSCAFG00000015634"; transcript_id "ENSCAFT00000024802.14"; transcript_name "ENSCAFT00000024802";
chr3    ucsc    exon    72230308    72230403    .   +   .   ID "ENSCAFT00000024802%3AE0"; Parent "ENSCAFT00000024802.14"; Name "ENSCAFT00000024802"; biotype "protein_coding"; gene_id "GENE13"; gene_name "ENSCAFG00000015634"; transcript_id "ENSCAFT00000024802.14"; exon_id "ENSCAFT00000024802%3AE0";
chr3    ucsc    exon    72257459    72257619    .   +   .   ID "ENSCAFT00000024802%3AE1"; Parent "ENSCAFT00000024802.14"; Name "ENSCAFT00000024802"; biotype "protein_coding"; gene_id "GENE13"; gene_name "ENSCAFG00000015634"; transcript_id "ENSCAFT00000024802.14"; exon_id "ENSCAFT00000024802%3AE1";
chr3    ucsc    exon    72272584    72272708    .   +   .   ID "ENSCAFT00000024802%3AE2"; Parent "ENSCAFT00000024802.14"; Name "ENSCAFT00000024802"; biotype "protein_coding"; gene_id "GENE13"; gene_name "ENSCAFG00000015634"; transcript_id "ENSCAFT00000024802.14"; exon_id "ENSCAFT00000024802%3AE2";

[1769mkc]

will give it a try thank you so much