How to prepare gene references for Cufflinks

g781

Member

Join Date: May 2010
Posts: 25

How to prepare gene references for Cufflinks

02-13-2013, 02:01 PM

Hi community

I am very confused to prepare the gene references for TopHat-Cufflinks.

Code:

Tb427_01_v4	EuPathDB	supercontig	1	1064569	.	+	.	"ID=Tb427_01_v4;Name=Tb427_01_v4;description=Tb427_01_v4;size=1064569;web_id=Tb427_01_v4;molecule_type=dsDNA;organism_name=Trypanosoma brucei;translation_table=11;topology=linear;localization=nuclear;Dbxref=EuPathDB:Tb427_01_v4,taxon:1854310"
Tb427_10_v5	EuPathDB	supercontig	1	4145152	.	+	.	"ID=Tb427_10_v5;Name=Tb427_10_v5;description=Tb427_10_v5;size=4145152;web_id=Tb427_10_v5;molecule_type=dsDNA;organism_name=Trypanosoma brucei;translation_table=11;topology=linear;localization=nuclear;Dbxref=EuPathDB:Tb427_10_v5,taxon:1854310"
Tb427_11_01_v4	EuPathDB	supercontig	1	4977113	.	+	.	"ID=Tb427_11_01_v4;Name=Tb427_11_01_v4;description=Tb427_11_01_v4;size=4977113;web_id=Tb427_11_01_v4;molecule_type=dsDNA;organism_name=Trypanosoma brucei;translation_table=11;topology=linear;localization=nuclear;Dbxref=EuPathDB:Tb427_11_01_v4,taxon:1854310"
Tb427_01_v4	EuPathDB	gene	57396	59181	.	-	.	ID=Tb427.01.100;Name=Tb427.01.100;description=RNA+polymerase+%28pseudogene%29%2C+putative;size=1786;web_id=Tb427.01.100;locus_tag=Tb427.01.100;size=1786
Tb427_01_v4	EuPathDB	mRNA	57396	59181	.	-	.	"ID=rna_Tb427.01.100-1;Name=Tb427.01.100-1;description=Tb427.01.100-1;size=1786;Parent=Tb427.01.100;Ontology_term=GO:0003899,GO:0006350,GO:0032549;Dbxref=EuPathDB:Tb427.01.100,taxon:1854310"
Tb427_01_v4	EuPathDB	CDS	59086	59181	.	-	0	ID=cds_Tb427.01.100-1;Name=cds;description=.;size=96;Parent=rna_Tb427.01.100-1
Tb427_01_v4	EuPathDB	CDS	57396	59081	.	-	0	ID=cds_Tb427.01.100-1;Name=cds;description=.;size=1686;Parent=rna_Tb427.01.100-1
Tb427_01_v4	EuPathDB	exon	59086	59181	.	-	.	ID=exon_Tb427.01.100-1;Name=exon;description=exon;size=96;Parent=rna_Tb427.01.100-1
Tb427_01_v4	EuPathDB	exon	57396	59081	.	-	.	ID=exon_Tb427.01.100-2;Name=exon;description=exon;size=1686;Parent=rna_Tb427.01.100-1
Tb427_01_v4	EuPathDB	gene	289975	291237	.	+	.	ID=Tb427.01.1000;Name=Tb427.01.1000;description=developmentally+regulated+phosphoprotein;size=1263;web_id=Tb427.01.1000;locus_tag=Tb427.01.1000;size=1263
Tb427_01_v4	EuPathDB	mRNA	289975	291237	.	+	.	"ID=rna_Tb427.01.1000-1;Name=Tb427.01.1000-1;description=Tb427.01.1000-1;size=1263;Parent=Tb427.01.1000;Ontology_term=GO:0005524;Dbxref=EuPathDB:Tb427.01.1000,NCBI_gi:261326019,taxon:1854310"
Tb427_01_v4	EuPathDB	CDS	289975	291237	.	+	0	ID=cds_Tb427.01.1000-1;Name=cds;description=.;size=1263;Parent=rna_Tb427.01.1000-1
Tb427_01_v4	EuPathDB	exon	289975	291237	.	+	.	ID=exon_Tb427.01.1000-1;Name=exon;description=exon;size=1263;Parent=rna_Tb427.01.1000-1
Tb427_01_v4	EuPathDB	gene	291667	293826	.	+	.	ID=Tb427.01.1010;Name=Tb427.01.1010;description=hypothetical+protein%2C+conserved;size=2160;web_id=Tb427.01.1010;locus_tag=Tb427.01.1010;size=2160
Tb427_01_v4	EuPathDB	mRNA	291667	293826	.	+	.	"ID=rna_Tb427.01.1010-1;Name=Tb427.01.1010-1;description=Tb427.01.1010-1;size=2160;Parent=Tb427.01.1010;Ontology_term=GO:0008270;Dbxref=EuPathDB:Tb427.01.1010,taxon:1854310"
Tb427_01_v4	EuPathDB	CDS	291667	293826	.	+	0	ID=cds_Tb427.01.1010-1;Name=cds;description=.;size=2160;Parent=rna_Tb427.01.1010-1
Tb427_01_v4	EuPathDB	exon	291667	293826	.	+	.	ID=exon_Tb427.01.1010-1;Name=exon;description=exon;size=2160;Parent=rna_Tb427.01.1010-1
Tb427_01_v4	EuPathDB	gene	294311	295591	.	+	.	ID=Tb427.01.1020;Name=Tb427.01.1020;description=hypothetical+protein%2C+conserved;size=1281;web_id=Tb427.01.1020;locus_tag=Tb427.01.1020;size=1281
Tb427_01_v4	EuPathDB	mRNA	294311	295591	.	+	.	"ID=rna_Tb427.01.1020-1;Name=Tb427.01.1020-1;description=Tb427.01.1020-1;size=1281;Parent=Tb427.01.1020;Dbxref=EuPathDB:Tb427.01.1020,taxon:1854310"
Tb427_01_v4	EuPathDB	CDS	294311	295591	.	+	0	ID=cds_Tb427.01.1020-1;Name=cds;description=.;size=1281;Parent=rna_Tb427.01.1020-1
Tb427_01_v4	EuPathDB	exon	294311	295591	.	+	.	ID=exon_Tb427.01.1020-1;Name=exon;description=exon;size=1281;Parent=rna_Tb427.01.1020-1
Tb427_01_v4	EuPathDB	gene	297053	298426	.	+	.	ID=Tb427.01.1030;Name=Tb427.01.1030;description=hypothetical+protein%2C+conserved;size=1374;web_id=Tb427.01.1030;locus_tag=Tb427.01.1030;size=1374

... ... ...

Tb427_09_v4	EuPathDB	rRNA	281365	281579	.	-	.	ID=rna_Tb427.02.1520-1;Name=Tb427.02.1520-1;description=Tb427.02.1520-1;size=215;Parent=Tb427.02.1520;Dbxref=EuPathDB:Tb427.02.1520,taxon:1854310
Tb427_02_v4	EuPathDB	snRNA	1025274	1025348	.	+	.	ID=rna_Tb427.02.5680-1;Name=Tb427.02.5680-1;description=Tb427.02.5680-1;size=75;Parent=Tb427.02.5680;Dbxref=EuPathDB:Tb427.02.5680,taxon:1854310
Tb427_04_v4	EuPathDB	tRNA	318221	318292	.	-	.	ID=rna_Tb427.04.1195-1;Name=Tb427.04.1195-1;description=Tb427.04.1195-1;size=72;Parent=Tb427.04.1195;Dbxref=EuPathDB:Tb427.04.1195,taxon:1854310
Tb427_04_v4	EuPathDB	snRNA	326071	326164	.	+	.	ID=rna_Tb427.04.1213-1;Name=Tb427.04.1213-1;description=Tb427.04.1213-1;size=94;Parent=Tb427.04.1213;Dbxref=EuPathDB:Tb427.04.1213,taxon:1854310
Tb427_04_v4	EuPathDB	scRNA_encoding	1287901	1287973	.	-	.	ID=rna_Tb427.04.4663:scRNA-1;Name=Tb427.04.4663%3AscRNA-1;description=Tb427.04.4663%3AscRNA-1;size=73;Parent=Tb427.04.4663:scRNA;Dbxref=EuPathDB:Tb427.04.4663:scRNA,taxon:1854310
Tb427_08_v4	EuPathDB	transcript	861170	861430	.	-	.	ID=rna_Tb427.08.2861-1;Name=Tb427.08.2861-1;description=Tb427.08.2861-1;size=261;Parent=Tb427.08.2861;Dbxref=EuPathDB:Tb427.08.2861,taxon:1854310

My gene references look as above. I've run TopHat with full gene references. Now I am running Cufflinks pipeline with -M mask.gff to exclude rows, I don't need except for 4 types of gene, mRNA, CDS and exon.

My questions are:
1) Do I use the gene references correctly? or I just need to run TopHat with gene reference with gene/mRNA/CDS/exon?

2) I've checked few gene reference files provided by Cufflinks website, e.g. yeast. Those files only provide rows for both types of CDS and exon (I don't consider the TSS and TTS). What is the difference between references with "gene/mRNA/CDS/exon" and with "CDS/exon"? As my know, the gene can include multiple mRNAs, which can include multiple CDSs, so the region of gene should cover all of its mRNAs/CDSs. If I don't tell Cufflinks the region of gene, how Cufflinks know the gene's location by a reference file with "CDS/exon".

3) In question 2), for the reference with "gene/mRNA/CDS/exon" and with "CDS/exon", which one do you prefer when you use Cufflinks?

PS: I mean Cufflinks that is a pipeline including cufflinks, cuffdiff ... ...

Many thanks in advance.

Tags: None

g781

Member

Join Date: May 2010

Posts: 25
Share

Post
#2

02-13-2013, 03:37 PM

Hi all,

It turns out that the annotation from Cufflinks website is in GTF2 format, whereas my annotation is in GFF3 format.

I did a comparison between both files by converting the GFF3 to GTF2. So the items in GFT2 should be the same the GFF3 with CDS/exon except warning items.

Anyway. I think I should redo my job from TopHat to Cufflinks again.

Thanks everyone.
Comment

Previous template Next

Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t

by SEQadmin2

Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...
- Channel: Articles
10-14-2026, 09:55 AM
New Genomics Technologies Take Aim at Long-Standing Limits

by SEQadmin2

Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
- Channel: Articles
09-28-2026, 10:25 AM

Topics	Statistics	Last Post
Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2 Started by SEQadmin2, Yesterday, 10:52 AM	0 responses 9 views 0 reactions	Last Post by SEQadmin2 Yesterday, 10:52 AM
Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2 Started by SEQadmin2, 10-14-2026, 05:39 AM	0 responses 19 views 0 reactions	Last Post by SEQadmin2 10-14-2026, 05:39 AM
Larger Datasets Reveal Additional Switches That Control Gene Expression by SEQadmin2 Started by SEQadmin2, 10-13-2026, 09:56 AM	0 responses 16 views 0 reactions	Last Post by SEQadmin2 10-13-2026, 09:56 AM
Computational Tool Captures How Chromatin Folds at Scale by SEQadmin2 Started by SEQadmin2, 10-09-2026, 11:14 AM	0 responses 27 views 0 reactions	Last Post by SEQadmin2 10-09-2026, 11:14 AM

Unconfigured Ad

How to prepare gene references for Cufflinks

Comment

Latest Articles

ad_right_rmr

News