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plagnollab / RNASeq_pipeline

Set of scripts for RNA-Seq data processing
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read.HTSeqCounts #3

Closed kittyl closed 7 years ago

kittyl commented 9 years ago

The latest version of DEXSeq no longer has this function. It has been replaced with DEXSeqDataSetFromHTSeq Will need to fix.

vplagnol commented 9 years ago

Yes, I think I replaced that in the dexseq pipeline. But perhaps not the deseq steps. I was thinking of reading the deseq vignette to see how they suggest to do it.

On Thu, Feb 5, 2015 at 10:09 AM, kittyl notifications@github.com wrote:

The latest version of DEXSeq no longer has this function. It has been replaced with DEXSeqDataSetFromHTSeq Will need to fix.

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/3.

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/

kittyl commented 9 years ago

Ok. I think it would still be good if we can keep the counts_prepare part separate from the deseq and dexseq analysis.

vplagnol commented 9 years ago

Yes I think it is a good idea, just needs a bit of tweaking.

On Thu, Feb 5, 2015 at 10:46 AM, kittyl notifications@github.com wrote:

Ok. I think it would still be good if we can keep the counts_prepare part separate from the deseq and dexseq analysis.

— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/3#issuecomment-73027269 .

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol