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Search: Posts Made By: Gordona
Forum: Bioinformatics 05-23-2016, 01:50 AM
Replies: 1
Views: 888
Posted By Gordona
If you knew what version release you used as your...

If you knew what version release you used as your reference genome that would help find the annotation to go with it. For example on Ensembl Plants you can download GFF3 files for version 31:...
Forum: RNA Sequencing 07-21-2015, 03:22 AM
Replies: 0
Views: 967
Posted By Gordona
Combining >two mappings (reference and de novo) in hexaploid wheat

Hi there,
Has anyone combined more than one mapping data set when analysing with DESeq2 or EdgeR?

We are looking at the interaction of a fungus and hexaploid wheat as an infection takes place...
Forum: RNA Sequencing 06-27-2014, 04:01 AM
Replies: 1
Views: 1,295
Posted By Gordona
getting data into DESeq2

Hi there,
i've got R version 3.1.0
DESeq2 version 1.4.5

I'm trying to get my data into R to create a DESeq object and i've tried following the vignette to work out how I may put my data in...
Forum: RNA Sequencing 06-20-2014, 01:21 AM
Replies: 3
Views: 2,103
Posted By Gordona
Dear Simon, Thanks for the advice, will get...

Dear Simon,

Thanks for the advice, will get DESeq2 now.. and i'm sure i'll post again (with full info pasted in)

Anna
Forum: RNA Sequencing 06-20-2014, 01:18 AM
Replies: 3
Views: 2,103
Posted By Gordona
Same data in R studio worked

Just thought i'd give an update to my earlier post

..i've just put exactly the same data and code into R studio after installing the DESeq package and it's worked and given me the library size....
Forum: RNA Sequencing 06-20-2014, 12:11 AM
Replies: 3
Views: 2,103
Posted By Gordona
DESeq teething problems/errors

Hi there,
I've installed R (version 3.1.10) and DESeq(1.16.0) yesterday.
I've got my counts table and experimental design in, but when I try to estimateSizeFactors I get the following error:

>...
Forum: RNA Sequencing 04-24-2014, 07:16 AM
Replies: 0
Views: 1,343
Posted By Gordona
RNA-seq wheat-fungal timecourse

Hi there,
I'm finally posting rather than viewing as i'd appreciate some advice about my big experiment.

I am looking at the interaction of hexaploid wheat and a fungal pathogen Claviceps...
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