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Forum: RNA Sequencing 08-12-2016, 01:17 AM
Replies: 9
Views: 3,036
Posted By chc*
Normalising metatranscriptomic data with metagenomic data

Hi Brian, I am currently setting up such an experiment as you suggest above where I want to know "who is doing what" in a community under two different conditions. Your suggestion is exactly what I...
Forum: RNA Sequencing 06-02-2016, 06:56 AM
Replies: 0
Views: 1,115
Posted By chc*
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...
Forum: RNA Sequencing 05-25-2016, 05:21 AM
Replies: 3
Views: 1,161
Posted By chc*
Total RNA was prepared by grinding a frozen...

Total RNA was prepared by grinding a frozen pellet followed by the Ambion ToTALLY RNA kit. cDNA libraries were prepared after double depletion of rRNA using the plant, then bacterial RiboZero kits.
Forum: RNA Sequencing 05-25-2016, 04:18 AM
Replies: 3
Views: 1,161
Posted By chc*
Bacterial signal in metatranscriptome data

Hi all. I have some RNA-Seq data from the sequencing of a green algae in co- culture with a bacterium. The bacterial cell numbers were reported to be in a 50:1 ratio with the green algae. However,...
Forum: Bioinformatics 03-31-2016, 04:34 AM
Replies: 2
Views: 1,547
Posted By chc*
Transrate for metatranscriptome data

Hi all,

I am trying to install and use Transrate to assess the quality of different assemblies of some metatranscriptome data I have. However when I use gem install and then try to install...
Forum: Bioinformatics 02-11-2016, 03:33 AM
Replies: 1
Views: 2,622
Posted By chc*
MEGAN 6 Community Edition won't launch

Hi all.

I installed MEGAN 6 Community Edition as below on my Linux system (Fedora 23, java version 1.8.0_71). However I cannot get MEGAN 6 GUI to launch. I just get a new line with no error...
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