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Novel gene with overlapping coordinates by using reference annotation #164

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zpliu1126 opened this issue Mar 12, 2024 · 5 comments
Closed

Novel gene with overlapping coordinates by using reference annotation #164

zpliu1126 opened this issue Mar 12, 2024 · 5 comments
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enhancement New feature or request

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@zpliu1126
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Hi~ Andrey,

After updating the GFF annotation with Isoquant, I found many Novelgenes with overlapping coordinates when I used Stringtie to calculate the gene expression downstream. I guess these may be different transcripts of the same gene, and they are not well combined.

#* example of novel gene
cat  A2.extended_annotation.gtf|grep 108761523|awk '$3=="gene"{print $0}'

###########restul##############
Chr12	IsoQuant	gene	108761523	108762488	.	+	.	gene_id "novel_gene_Chr12_177202"; transcripts "1"; 
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177104"; transcripts "1"; 
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177106"; transcripts "1"; 
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177152"; transcripts "1"; 
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177154"; transcripts "1";

Best
zpliu
@andrewprzh
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Dear @zpliu1126

Current gene detection algorithm is based purely on spliced sites shared between transcripts. Probably, using exonic overlaps also makes sense.
Could you send all GTF lines for these genes?

Best
Andrey

@andrewprzh andrewprzh added the enhancement New feature or request label Mar 12, 2024
@zpliu1126
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Hi~ Andrey,
Here are a few examples.

Chr12	IsoQuant	gene	108761523	108762488	.	+	.	gene_id "novel_gene_Chr12_177202"; transcripts "1"; 
Chr12	IsoQuant	transcript	108761523	108762488	.	+	.	gene_id "novel_gene_Chr12_177202"; transcript_id "transcript177201.Chr12.nnic"; exons "2";
Chr12	IsoQuant	exon	108761523	108761897	.	+	.	gene_id "novel_gene_Chr12_177202"; transcript_id "transcript177201.Chr12.nnic"; exon "1"; exon_id "Chr12.19656";
Chr12	IsoQuant	exon	108762093	108762488	.	+	.	gene_id "novel_gene_Chr12_177202"; transcript_id "transcript177201.Chr12.nnic"; exon "2"; exon_id "Chr12.19657";
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177104"; transcripts "1"; 
Chr12	IsoQuant	transcript	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177104"; transcript_id "transcript177103.Chr12.nnic"; exons "4";
Chr12	IsoQuant	exon	108761523	108762836	.	+	.	gene_id "novel_gene_Chr12_177104"; transcript_id "transcript177103.Chr12.nnic"; exon "1"; exon_id "Chr12.19658";
Chr12	IsoQuant	exon	108762965	108763841	.	+	.	gene_id "novel_gene_Chr12_177104"; transcript_id "transcript177103.Chr12.nnic"; exon "2"; exon_id "Chr12.19659";
Chr12	IsoQuant	exon	108764126	108764230	.	+	.	gene_id "novel_gene_Chr12_177104"; transcript_id "transcript177103.Chr12.nnic"; exon "3"; exon_id "Chr12.19660";
Chr12	IsoQuant	exon	108764509	108765123	.	+	.	gene_id "novel_gene_Chr12_177104"; transcript_id "transcript177103.Chr12.nnic"; exon "4"; exon_id "Chr12.19661";
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177106"; transcripts "1"; 
Chr12	IsoQuant	transcript	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177106"; transcript_id "transcript177105.Chr12.nnic"; exons "4";
Chr12	IsoQuant	exon	108761523	108762836	.	+	.	gene_id "novel_gene_Chr12_177106"; transcript_id "transcript177105.Chr12.nnic"; exon "1"; exon_id "Chr12.19658";
Chr12	IsoQuant	exon	108762965	108763841	.	+	.	gene_id "novel_gene_Chr12_177106"; transcript_id "transcript177105.Chr12.nnic"; exon "2"; exon_id "Chr12.19659";
Chr12	IsoQuant	exon	108764126	108764230	.	+	.	gene_id "novel_gene_Chr12_177106"; transcript_id "transcript177105.Chr12.nnic"; exon "3"; exon_id "Chr12.19660";
Chr12	IsoQuant	exon	108764864	108765123	.	+	.	gene_id "novel_gene_Chr12_177106"; transcript_id "transcript177105.Chr12.nnic"; exon "4"; exon_id "Chr12.19662";
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177152"; transcripts "1"; 
Chr12	IsoQuant	transcript	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177152"; transcript_id "transcript177151.Chr12.nnic"; exons "3";
Chr12	IsoQuant	exon	108761523	108762836	.	+	.	gene_id "novel_gene_Chr12_177152"; transcript_id "transcript177151.Chr12.nnic"; exon "1"; exon_id "Chr12.19658";
Chr12	IsoQuant	exon	108762965	108764230	.	+	.	gene_id "novel_gene_Chr12_177152"; transcript_id "transcript177151.Chr12.nnic"; exon "2"; exon_id "Chr12.19663";
Chr12	IsoQuant	exon	108764509	108765123	.	+	.	gene_id "novel_gene_Chr12_177152"; transcript_id "transcript177151.Chr12.nnic"; exon "3"; exon_id "Chr12.19661";
Chr12	IsoQuant	gene	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177154"; transcripts "1"; 
Chr12	IsoQuant	transcript	108761523	108765123	.	+	.	gene_id "novel_gene_Chr12_177154"; transcript_id "transcript177153.Chr12.nnic"; exons "3";
Chr12	IsoQuant	exon	108761523	108762836	.	+	.	gene_id "novel_gene_Chr12_177154"; transcript_id "transcript177153.Chr12.nnic"; exon "1"; exon_id "Chr12.19658";
Chr12	IsoQuant	exon	108762965	108764230	.	+	.	gene_id "novel_gene_Chr12_177154"; transcript_id "transcript177153.Chr12.nnic"; exon "2"; exon_id "Chr12.19663";
Chr12	IsoQuant	exon	108764864	108765123	.	+	.	gene_id "novel_gene_Chr12_177154"; transcript_id "transcript177153.Chr12.nnic"; exon "3"; exon_id "Chr12.19662";
Chr12	IsoQuant	exon	108761668	108761897	.	+	.	gene_id "novel_gene_Chr12_177166"; transcript_id "transcript177165.Chr12.nnic"; exon "1"; exon_id "Chr12.19664";
Chr12	IsoQuant	exon	108762084	108762488	.	+	.	gene_id "novel_gene_Chr12_177166"; transcript_id "transcript177165.Chr12.nnic"; exon "2"; exon_id "Chr12.19665";
Chr12	IsoQuant	gene	108761721	108765123	.	+	.	gene_id "novel_gene_Chr12_177188"; transcripts "1"; 
Chr12	IsoQuant	transcript	108761721	108765123	.	+	.	gene_id "novel_gene_Chr12_177188"; transcript_id "transcript177187.Chr12.nnic"; exons "3";
Chr12	IsoQuant	exon	108761721	108762618	.	+	.	gene_id "novel_gene_Chr12_177188"; transcript_id "transcript177187.Chr12.nnic"; exon "1"; exon_id "Chr12.19667";
Chr12	IsoQuant	exon	108762699	108762836	.	+	.	gene_id "novel_gene_Chr12_177188"; transcript_id "transcript177187.Chr12.nnic"; exon "2"; exon_id "Chr12.19668";
Chr12	IsoQuant	exon	108762965	108765123	.	+	.	gene_id "novel_gene_Chr12_177188"; transcript_id "transcript177187.Chr12.nnic"; exon "3"; exon_id "Chr12.19669";

Best
zpliu

@zpliu1126
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Dear @zpliu1126

Current gene detection algorithm is based purely on spliced sites shared between transcripts. Probably, using exonic overlaps also makes sense. Could you send all GTF lines for these genes?

Best Andrey

I haven used gffread to merge those transcripts.

 gffread  -M  --cluster-only isoquant.gff >isoquant_collapse.gff

Best
zpliu

@andrewprzh
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@zpliu1126

Thanks for the data, at looks that at least some transcripts share splice sites. I'll try to improve the algorithm for detecting same-gene transcripts.

Best
Andrey

@andrewprzh
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Novel gene merging strategy is completely reworked in IsoQuant 3.4, should be fixed now.

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