Martin Reczko <reczko@fleming.gr>
22122016
to Maria, Panagiotis, Panagiotis 
Dear all,

as Panagiotis kindly helped to set up the quant-seq pipeline on our cluster,
here is the first analysis with the new setup.
As discussed, the outlier (sample 24) has been removed and 2 more contrasts have been added:
http://genomics-lab.fleming.gr/fleming/GKlab/run307/metaseqr_quantseq_ms_deseq_22122016/

Best wishes and happy holidays,
Martin


Panagiotis Chouvardas
Dec 16 (6 days ago)

to me, Maria 
Hi Martin,

We would like to have a couple of more comparisons for Maria Sakkou quant-seq data. The groups we would like to compare are:  group1 with group4 (group 1 control) and group5 with group8 (group5 control).

Have you developed  an optimized differential analysis pipeline for quant-seq data? Because I guess in the future this may be needed again and in order not to trouble you and Panagiotis all the time can you share with me the workflow (mostly the part from the raw read count matrix and forward so we will have consistent analysis in all comparisons)? 

Thanks a lot in advance,

Dear all,

at
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=fa&hubUrl=http://genomics-lab.fleming.gr/fleming/GKlab/run307/hub.txt
you will find tracks for the 24 samples, normalized to the smallest library with
TNF_DeltaARE_ColVI_p75_f_vs_f_1_SFs  (GK3R63-MS10) with 2860948 reads.
At
http://genomics-lab.fleming.gr/fleming/GKlab/run307
you will find the bam files with reads and alignments (for Panagiotis).

Best wishes,
Martin