Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file

Question

[Muhammad]

Dear All, I want to do some comparative genomics analysis using cattle and Buffalo Genome GTF and GFF files. Can some body share the URL for it ? I searched NCBI but i found that refseq file for all of three reference genomes in NCBI uses contig assembly number something like this

NC_037328.1 RefSeq  region  1   158534110   .   +   .   ID=NC_037328.1:1..158534110;Dbxref=taxon:9913;Name=1;breed=Hereford;chromosome=1;gbkey=Src;genome=chromosome;isolate=L1 Dominette 01449 registration number 42190680;mol_type=genomic DNA;sex=female;tissue-type=left lung
NC_037328.1 Gnomon  pseudogene  207933  217580  .   -   .   ID=gene-LOC112

But I want GTF files with chromsome number someting like this

chr1    ncbiRefSeq  transcript  210759  214966  .   -   .   gene_id "LOC112447072"; transcript_id "XR_003035142.1";  gene_name "LOC112447072";
chr1    ncbiRefSeq  exon    210759  212235  .   -   .   gene_id "LOC112447072"; transcript_id "XR_003035142.1"; exon_number "1"; exon_id "XR_003035142.1.1"; gene_name "LOC112447072";
chr1    ncbiRefSeq  exon    212941  213154  .   -   .   gene_id "LOC112447072"; transcript_id "XR_003035142.1"; exon_number "2"; exon_id "XR_003035142.1.2"; gene_name "LOC112447072";
chr1    ncbiRefSeq  exon    214935  214966  .   -   .   gene_id "LOC112447072"; transcript_id "XR_003035142.1"; exon_number "3"; exon_id "XR_003035142.1.3"; gene_name "LOC112447072";
chr1    ncbiRefSeq  transcript  217517  257046  .   -   .   gene_id "LOC101903639"; transcript_id "XR_003035135.1";  gene_name "LOC101903639";
chr1    ncbiRefSeq  exon    217517  219285  .   -   .   gene_id "LOC101903639"; transcript_id "XR_003035135.1"; exon_number "1"; exon_id "XR_003035135.1.1"; gene_name "LOC101903639";
chr1    ncbiRefSeq  exon    229250  229332  .   -

where can i find this please share a URL for this NCBI URL or other URL OR some solution for it ? Also an additional Question if i want to work with some genome whose file dont exists how can i found or made it ?

[kalavattam]

One solution is to find and use tables to convert the RefSeq identifiers to standard chromosome numbers. For example, there's a table here you could use to convert the identifiers in your GTF file to standard chromosome names prefixed with “chr”:

#!/usr/bin/env bash

#  Save the mapping table to a TXT file
printf \
"1\tNC_037328.1\n\
2\tNC_037329.1\n\
3\tNC_037330.1\n\
4\tNC_037331.1\n\
5\tNC_037332.1\n\
6\tNC_037333.1\n\
7\tNC_037334.1\n\
8\tNC_037335.1\n\
9\tNC_037336.1\n\
10\tNC_037337.1\n\
11\tNC_037338.1\n\
12\tNC_037339.1\n\
13\tNC_037340.1\n\
14\tNC_037341.1\n\
15\tNC_037342.1\n\
16\tNC_037343.1\n\
17\tNC_037344.1\n\
18\tNC_037345.1\n\
19\tNC_037346.1\n\
20\tNC_037347.1\n\
21\tNC_037348.1\n\
22\tNC_037349.1\n\
23\tNC_037350.1\n\
24\tNC_037351.1\n\
25\tNC_037352.1\n\
26\tNC_037353.1\n\
27\tNC_037354.1\n\
28\tNC_037355.1\n\
29\tNC_037356.1\n\
X\tNC_037357.1\n\
Y\tNC_082638.1\n\
MT\tNC_006853.1\n" \
    > chr_map.txt

#  Convert identifiers in the GTF file
awk 'NR==FNR { map[$2] = "chr" $1; next } $1 in map { $1 = map[$1] }1' \
    chr_map.txt \
    original.gtf \
        > converted.gtf

Also an additional Question if i want to work with some genome whose file dont exists how can i found or made it ?

I’m not entirely sure what you’re asking. If a genome file doesn’t exist (for example, if it’s for an organism that hasn’t been sequenced), then there won’t be a way for you to find or generate it.

[kalavattam]

Also, it looks like this bison release only includes scaffolds and lacks assembled chromosomes (except for the mitochondrial chromosome).