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Search: Posts Made By: christophe
Forum: Bioinformatics 09-08-2014, 02:02 PM
Replies: 648
Views: 191,006
Posted By christophe
Hi Andrew and Felix, Sorry for this late...

Hi Andrew and Felix,

Sorry for this late message.

Thanks Andrew for your reply to my question regarding M-bias.
I effectively ran the Extractor with the --no_overlap option on before. As...
Forum: Bioinformatics 08-22-2014, 04:21 PM
Replies: 648
Views: 191,006
Posted By christophe
Arrow M-bias: CHH and CHG total calls drop off in Read2

Hi Everyone,

I have questions regarding M-bias plot and CHH,CHG methylation calls generated with bismark. I hope it is the right thread to ask otherwise let me know where should have I posted it....
Forum: Bioinformatics 03-12-2012, 10:24 AM
Replies: 5
Views: 3,409
Posted By christophe
Hi Loyal, That works. Only reshape2 was...

Hi Loyal,
That works.
Only reshape2 was loading automatically and not reshape.
Thanks
Christophe
Forum: Bioinformatics 03-11-2012, 11:47 PM
Replies: 5
Views: 3,409
Posted By christophe
Addendum to my previous post: I have tried to...

Addendum to my previous post:
I have tried to run cummeRbund both on linux and Windows and got the same error:

Error in as.data.frame(cast(genemelt, ... ~ measurement)) :
could not find...
Forum: Bioinformatics 03-11-2012, 11:45 PM
Replies: 5
Views: 3,409
Posted By christophe
Hi loyal Goff, I have been trying running...

Hi loyal Goff,
I have been trying running CummeRbund. As suggested I installed the latest version of cummeRbund (v1.1.3) within R 2.15.0 . The Error << Error in data.frame(index =...
Forum: Literature Watch 02-02-2012, 09:57 AM
Replies: 25
Views: 8,939
Posted By christophe
Hi Stefano, Thanks for the CNAnorm Package. ...

Hi Stefano,
Thanks for the CNAnorm Package.

As PeakPloidy is really computationally time consuming, is there a way to run it as a parallel job (multithreading) using an R package such as "snow" ...
Forum: Bioinformatics 03-30-2011, 08:04 PM
Replies: 25
Views: 14,209
Posted By christophe
Question Overlapping and non-Overlapping pair-end reads with Tophat

Hi Cole,
First, According to the quote above, we may use negative inner distance. If I set it up at -30 and the stddev at 10, this mean tophat will look for overlapping of size 20 to 40.
Am I...
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