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Using MapMan

RNAseq data

RNAseq data
Answer
7/7/10 1:09 PM
Dear MapMan users,
I was wondering if anybody ever analyzed a complete transcriptome data set generated by the Illumina genome analyzer or by 454 sequencing with MapMan? I am an absolute beginner in this field but guess the software would be really helpful for this type of data.

Cheers,
Anja

RE: RNAseq data
Answer
8/6/10 4:08 PM as a reply to Anja Paschold.
Dear Anja,

this depends on what you want to do...
But as the output of many popluar software tools (DESEQ, edgeR) is now very similar to microarray there is not a lot of difference (log2 Fc, adjusted p-values etc)

The only thing you have to be thoughtful of is the length bias for DE detection levels for PageMan analyses (as you will find more DE genes for longer genes and these might not be an unbiased sample of the gene universe)

See Young et al Genome Biology 2010, 11:R14.

But if you talk about actually determining DE genes, library biases etc for Arrays we have this in Robin now but RNAseq still requires R/bioC feel free to contact us for these questions per plain mail.



Best Wishes,
Bjrön

PS Maize mapping is in progress

RE: RNAseq data
Answer
2/28/11 7:03 AM as a reply to Björn Usadel.
Hi,
I would like to visualize RNA-Seq timecourse data using the metabolism_overview pathway map. What format do I need my file to be in?
I have gene_ids and transcript levels across time.
Thanks,
KC