Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Counting read depth using bedtools Kaas Bioinformatics 4 02-21-2014 07:12 PM
Count C versus read length EpiBrass Bioinformatics 1 01-28-2014 12:58 AM
Counting CpG's per read, please check my logic. Heisman General 4 10-15-2013 06:14 AM
Counting number of short-read cover positions d_t_nguyen Bioinformatics 4 06-24-2013 12:55 AM
Using DESeq with Biological Replicates with Different RNAseq Read Lengths jbvt Bioinformatics 3 05-21-2013 07:34 AM

Thread Tools
Old 06-02-2016, 06:56 AM   #1
Junior Member
Location: Devon, UK

Join Date: Jan 2016
Posts: 6
Default Read counting and DESeq versus read abundance with MG-RAST

Hi all.
I am planning a metatranscriptomics experiment to investigate the changes in community and metabolic function of a Chlorella culture and it's associated bacterial consortium. Practical aspects of preparing the libraries aside, I want to gain some clarity on the following:
Do I go for simple mapping of reads to annotated genes using MG-RAST then use the abundance automatically computed here for statistical inference of changes in transcript abundance? Alternatively, i can sequence the metagenome. My understanding is that if it is simple I can then map the RNAseq metatranscriptomic reads to a metagenomic assembly (or assembled genomes found within the metagenome) then use HTseq count and DESeq for DE analysis.
What are the pros and cons/ what are the reasons for chosing one or the other please?
chc* is offline   Reply With Quote

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 09:44 PM.

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