Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Newsbot! Literature Watch 3 07-31-2011 07:08 PM

Thread Tools
Old 05-04-2017, 03:36 AM   #1
Junior Member
Location: India

Join Date: May 2017
Posts: 1
Default RNA Seq analysis

I want to extract differential expressed genes using LIMMA from RNA seq data for three cancer types viz breast, lung and prostate. These data should have tumor and normal samples. I have read some papers which have used data from TCGA. BUt now TCGA has linked to Genomics Data Commons and all data are not open access. All BAM files are under controlled access. Also, LIMMA requires raw read counts for analysis. I an new to RNA seq data and analysis. Can anyone help, where should I get these data and what format should it be, as I have read that TPM, FPKM normalized values cannot be input to LIMMA.
richaM is offline   Reply With Quote
Old 05-04-2017, 03:55 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,888

For reference cross-posted:
GenoMax is offline   Reply With Quote
Old 05-25-2017, 12:46 PM   #3
Location: New York

Join Date: Nov 2012
Posts: 49

I'm not sure what you'll have to do to get your data, but I can give you some advice on the RNA-seq part.

If you're starting with BAM files that means your reads are already aligned, if you start with reads (.fastq) you can map them yourself using any splice aware mapping tool. Assuming you have bam files though, you'll want to use a tool that extracts raw counts from the bam files. You'll need an annotation file (.gtf or gff format probably) and a counting tool. htseq-counts or featureCounts (in the RSubread package) are both good and widely used tools for extracting raw counts from BAM files, so start there and extract your counts.

Once you have gotten that far, then there are alot of tools like limma, deseq2, or edgeR that can use that data for analysis.
aprice67 is offline   Reply With Quote

limma, rna seq

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 10:08 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO