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Forum: RNA Sequencing 05-12-2013, 11:39 PM
Replies: 6
Views: 3,152
Posted By Daniel1977
thanks for that, IŽll look into it.

thanks for that, IŽll look into it.
Forum: Bioinformatics 04-01-2013, 08:53 AM
Replies: 1
Views: 1,179
Posted By Daniel1977
DESeq 'stabilazing' transformations usage

Hi,

IŽm a little puzzled about the 'Di erential analysis of count data : the
DESeq2 package' protocol

I was trying it with (only) two samples and got the DE results, then I tried the suggested...
Forum: RNA Sequencing 03-22-2013, 12:52 AM
Replies: 6
Views: 3,152
Posted By Daniel1977
Thanks Kris_143. Yes one can always use the...

Thanks Kris_143.

Yes one can always use the (a) option.

But if you want to use cuffdiff it seems like a better option to run cuffdiff with all the conditions so that the variance model is more...
Forum: RNA Sequencing 03-21-2013, 06:26 AM
Replies: 6
Views: 3,152
Posted By Daniel1977
Any comments at least for Q4 and Q5? cheers

Any comments at least for Q4 and Q5?
cheers
Forum: Bioinformatics 03-20-2013, 03:11 AM
Replies: 77
Views: 26,905
Posted By Daniel1977
how about fasta files?

Hi,
could anyone please modify the script so that it works with fasta files instead of fastq files?

many many thanks!
Forum: RNA Sequencing 03-20-2013, 02:19 AM
Replies: 6
Views: 3,152
Posted By Daniel1977
No Replicates Cuffdiff; How does the 'variability model good fit' apply? and other...

Hi,

I want to clarify (in my head of course) how the system works so that I can make the proper choices when I use it.

I have RNAseq data for several conditions, cell line with or without a...
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