gene_id and gene_name confusions

[shpyang]

Hi,

I am trying to generate a file with the start and end positions of all the known genes. I got the genes.gtf file from the Illumina igenomes. However, I am confused with what id/name I should use? For example, should I use gene_name or gene_id?

It is more confusing that the same gene_name (eg. gene_name: MIR1302-10) has more than one gene_id, and some of them belong to different chromosomes. Below I am attaching all the known exon for MIR1302-10, 6 of them are located on chromosome 1, 6 on chromosome 19 and 2 on chromosome 9.

My question is that what are the start and end position of this gene?

Any help will be appreciated!

1 lincRNA exon 29554 30039 . + .
1 lincRNA exon 30267 30667 . + .
1 miRNA exon 30366 30503 . + .
1 lincRNA exon 30564 30667 . + .
1 lincRNA exon 30976 31097 . + .
1 lincRNA exon 30976 31109 . + .
19 lincRNA exon 71161 71646 . + .
19 lincRNA exon 71786 72274 . + .
19 miRNA exon 71973 72110 . + .
19 lincRNA exon 72171 72274 . + .
19 lincRNA exon 72585 72706 . + .
19 lincRNA exon 72585 72719 . + .
9 antisense exon 27657 30445 . + .
9 antisense exon 30758 30891 . + .
V9
exon_id ENSE00001947070; exon_number 1; gene_biotype lincRNA; gene_id ENSG00000243485; gene_name MIR1302-10; transcript_id ENST00000473358; transcript_name MIR1302-10-001; tss_id TSS131500;
exon_id ENSE00001841699; exon_number 1; gene_biotype lincRNA; gene_id ENSG00000243485; gene_name MIR1302-10; transcript_id ENST00000469289; transcript_name MIR1302-10-002; tss_id TSS98838;
exon_id ENSE00001807514; exon_number 1; gene_biotype miRNA; gene_id ENSG00000221311; gene_name MIR1302-10; transcript_id ENST00000408384; transcript_name MIR1302-10-201; tss_id TSS12193;
exon_id ENSE00001922571; exon_number 2; gene_biotype lincRNA; gene_id ENSG00000243485; gene_name MIR1302-10; transcript_id ENST00000473358; transcript_name MIR1302-10-001; tss_id TSS131500;
exon_id ENSE00001827679; exon_number 3; gene_biotype lincRNA; gene_id ENSG00000243485; gene_name MIR1302-10; transcript_id ENST00000473358; transcript_name MIR1302-10-001; tss_id TSS131500;
exon_id ENSE00001890064; exon_number 2; gene_biotype lincRNA; gene_id ENSG00000243485; gene_name MIR1302-10; transcript_id ENST00000469289; transcript_name MIR1302-10-002; tss_id TSS98838;
exon_id ENSE00002870487; exon_number 1; gene_biotype lincRNA; gene_id ENSG00000267588; gene_name MIR1302-10; transcript_id ENST00000590978; transcript_name MIR1302-10-001; tss_id TSS121237;
exon_id ENSE00002808517; exon_number 1; gene_biotype lincRNA; gene_id ENSG00000267588; gene_name MIR1302-10; transcript_id ENST00000586110; transcript_name MIR1302-10-002; tss_id TSS12671;
exon_id ENSE00001808054; exon_number 1; gene_biotype miRNA; gene_id ENSG00000220978; gene_name MIR1302-11; transcript_id ENST00000408051; transcript_name MIR1302-11-201; tss_id TSS183898;
exon_id ENSE00002781923; exon_number 2; gene_biotype lincRNA; gene_id ENSG00000267588; gene_name MIR1302-10; transcript_id ENST00000590978; transcript_name MIR1302-10-001; tss_id TSS121237;
exon_id ENSE00002955681; exon_number 3; gene_biotype lincRNA; gene_id ENSG00000267588; gene_name MIR1302-10; transcript_id ENST00000590978; transcript_name MIR1302-10-001; tss_id TSS121237;
exon_id ENSE00002841773; exon_number 2; gene_biotype lincRNA; gene_id ENSG00000267588; gene_name MIR1302-10; transcript_id ENST00000586110; transcript_name MIR1302-10-002; tss_id TSS12671;
exon_id ENSE00001665848; exon_number 1; gene_biotype antisense; gene_id ENSG00000227518; gene_name MIR1302-10; transcript_id ENST00000422679; transcript_name MIR1302-10-001; tss_id TSS34887;
exon_id ENSE00001797394; exon_number 2; gene_biotype antisense; gene_id ENSG00000227518; gene_name MIR1302-10; transcript_id ENST00000422679; transcript_name MIR1302-10-001; tss_id TSS34887;

[dpryan]

You'll want to use the gene_id, since as you found, gene names aren't unique. At least you're using an Ensemble GTF, things are a mess if you tried this on one from UCSC!

[shpyang]

Thank you so much!

Is it a good idea to keep the protein-coding region only, so that there will be less confusion - suppose my goal to detect DE genes based on read counts? I know it is over-simplified to calculate read count based on start and end positions, but this is the first step. Thanks again!

[dpryan]

Well, if you really do just want to detect DE genes, then just use htseq-count and save yourself the hassle.

[shpyang]

I also have the paired Exome-seq data, that's why I need the positions. I will definitely try Htseq-count.
Thanks a lot!