@@

Dear Vagelis,

at 
http://genomics-lab.fleming.gr/fleming/GKlab/run213/cuff

you'll find the results of running Cufflinks/cuffdiff on
the same condition-pairs in the following dir/files:

cuffdiff_GKR14_0h_vs_GKR15_1h/gene_exp.diff
cuffdiff_GKR14_0h_vs_GKR16_3h/gene_exp.diff
cuffdiff_GKR14_0h_vs_GKR17_6h/gene_exp.diff
cuffdiff_GKR14_0h_vs_GKR18_24h/gene_exp.diff
cuffdiff_GKR14_0h_vs_GKR19_7d/gene_exp.diff

(All 3 replicates are used,
the name of the 1st replicate is used to identify the condition).

At 0h vs 7d, cuffdiff finds 70 sig. diff.exp. genes,
where MetaSeqR found only 1.

Best wishes,
Martin



Dear Vagelis,

at
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm9&hubUrl=http://genomics-lab.fleming.gr/fleming/GKlab/run213/hub.txt
you will find following stranded tracks, with 3 replicates merged and normalized to the smallest
condition (1hour) having 99750012 reads total.

T0h.bamplus  (norm. factor: 0.9007184698526043)
T0h.bamminus
T1h.bamplus  (norm. factor: 1.0
T1h.bamminus
T3h.bamplus  (norm. factor: 0.871762113128735)
T3h.bamminus
T6h.bamplus  (norm. factor: 0.9409525153157573)
T6h.bamminus
T24h.bamplus (norm. factor: 0.7753196757284724)
T24h.bamminus
T7d.bamplus  (norm. factor: 0.7889254276218506)
T7d.bamminus

Best wishes from
Martin




V. Ntoukos RNAseq, 18samples								
Samples		BCs	ION	Date	reads (mil)	ION	Date	reads (mil)
GKR14	I-0h	13	212	7/22/2015	42.15			
GKR15	I-1h	14	213	7/23/2015	?			
GKR16	I-3h	15	212	7/22/2015	49.30			
GKR17	I-6h	16	213	7/23/2015	?			
GKR18	I-24h	7	211	7/21/2015	43.74			
GKR19	I-7d	8	211	7/21/2015	37.46			
GKR20	II-0h	1	209	7/17/2015	49.56			
GKR21	II-1h	2	210	7/21/2015	38.26			
GKR22	II-3h	3	210	7/21/2015	47.03			
GKR23	II-6h	4	209	7/17/2015	39.55			
GKR24	II-24h	5	208	7/16/2015	39.64			
GKR25	II-7d	6	208	7/16/2015	51.42			
GKR26	III-0h	7	200	6/26/2015	19.03	201	7/3/2015	27.55
GKR27	III-1h	8	200	6/26/2015	18.65	201	7/3/2015	16.90
GKR28	III-3h	9	202	7/7/2015	18.10	205	7/8/2015	34.26
GKR29	III-6h	10	202	7/7/2015	22.42	205	7/8/2015	49.31
GKR30	III-24h	11	207	7/15/2015	43.83			
GKR31	III-7d	12	207	7/15/2015	35.96			


From: Evangelos Ntougkos <ntougkos@fleming.gr>
Date: Tue, Jul 21, 2015 at 4:58 PM
Subject: Re: GKlab run200-205
To: Pantelis Hatzis <hatzis@fleming.gr>


Great thanks!

And the answers are....

Stranded: YES please

Cufflinks: YES please (each timepoint to control which is 0h).

Thanks and let me know if you need more info.

V.