SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Easy to Use Tissue-Specific Gene Expression Database BioInfoRx RNA Sequencing 0 08-09-2013 10:14 AM
Comparison of Tissue specific expression (Rna-seq) detq182 Bioinformatics 0 05-19-2012 08:25 PM
Constructing library of tissue-specific genes johannes.helmuth RNA Sequencing 0 10-20-2011 03:20 AM

Reply
 
Thread Tools
Old 05-16-2016, 10:56 PM   #1
qoiopipq
Junior Member
 
Location: melbourne

Join Date: Apr 2016
Posts: 7
Default Tissue specific 3' UTRs using DEXSeq

I used IsoSCM to identify alternative 3' UTRs with different lengths in different tissue types(output files are GTFs containing tissue specific 3' UTRs), then I want to quantify the differential usage of these alternative 3' UTRs across different tissue types. I know that neither Ensembl nor UCSC GTF reference file contains the tissue specific 3' UTRs, so I tried to re-annotate IsoSCM output GTF files with reference GTF. The idea is that I want to get a GTF file containing all tissue specific 3' UTRs, which can be used for the following dexseq_count step.

But, if multiple 3' UTRs/terminal exons (same start site, different stop sites) are annotated with same transcript ID, dexseq_prepare_annotation will only include the longest one in the GFF output.
Here is an example of two possible 3' UTRs of gene Fubp1 in thymus GTF file:
Code:
chr3	sol	exon	152232395	152233253	.	+	.	gene_id "Fubp1"; gene_name "Fubp1"; p_id "P24872"; transcript_id "NM_057172"; tss_id "TSS5999";
chr3	sol	exon	152232395	152232485	.	+	.	gene_id "Fubp1"; gene_name "Fubp1"; p_id "P24872"; transcript_id "NM_057172"; tss_id "TSS5999";
Two different 3' UTRs of gene Fubp1 in liver GTF file:
Code:
chr3	sol	exon	152232395	152233965	.	+	.	gene_id "Fubp1"; gene_name "Fubp1"; p_id "P24872"; transcript_id "NM_057172"; tss_id "TSS5999";
chr3	sol	exon	152232395	152233885	.	+	.	gene_id "Fubp1"; gene_name "Fubp1"; p_id "P24872"; transcript_id "NM_057172"; tss_id "TSS5999";
One more 3' UTR of gene Fubp1 in spleen GTF file:
Code:
chr3	sol	exon	152232395	152232532	.	+	.	gene_id "Fubp1"; gene_name "Fubp1"; p_id "P24872"; transcript_id "NM_057172"; tss_id "TSS5999";
After merging them and put through dexseq_prepare_annotation step, I only got one exon to represent 3' UTR:
Code:
chr3	dexseq_prepare_annotation.py	exonic_part	152232395	152233965	.	+	.	transcripts "NM_057172"; exonic_part_number "018"; gene_id "Fubp1"
So, I am wondering how can I include all alternative 3' UTRs in the GFF file, then I can use it to count for the usage of these alternative 3' UTRs ??

Cheers
qoiopipq is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:50 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO