Dear Vasso, the comparison between the samples of run340 and run296 are at: http://genomics-lab.fleming.gr/fleming/GKlab/run340/metaseqr_quantseq_run340_omitGIH2_omitUI1_vs_run296_stranded/index.html BW, Martin #@ Dear Vasso, please excuse the delay due to several urgent assignments. The last analysis (run340), excluding the UI1 sample is at: http://genomics-lab.fleming.gr/fleming/GKlab/run340/metaseqr_quantseq_run340_omitGIH2_omitUI1_stranded/index.html I'll prepare the analysis GHIvsG (you meant GIHvsG, correct?) GILvsG TIvsT before Friday, if this is ok. BW, Martin #@ From: Vasiliki Koliaraki Date: Thu, Aug 24, 2017 at 4:18 PM Subject: Re: GKlab run340 QuantiSeq 3' mRNA-Seq analysis To: Martin Reczko Dear Martin, I was looking again at all the results and I was wondering if you could run the last analysis again (run340), excluding the UI1 sample. It is seems to be very different from the other two UI samples and I have checked genes that should be expressed and are not. Also, I was wondering if you could also do a comparison between the samples of run340 and my first run (run296). In this case I would be interested in the following comparisons: GHIvsG GILvsG TIvsT Do you think this is possible? Best Regards, Vasso #@ Dear Vasso, at http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/GKlab/run340/hub.txt you will find tracks for the samples in run340, (normalized to the 2nd smallest library, GK3R93-TI1 with 1446690 reads. The smallest library, GK3R96-UI1 is kept without sampling): sample n_reads GK3R87-GIH1 3233197 GK3R88-GIH2 2767650 GK3R89-GIH3 3325252 GK3R90-GIL1 2144636 GK3R91-GIL2 5038491 GK3R92-GIL3 4371139 GK3R93-TI1 1446690 GK3R94-TI2 1832812 GK3R95-TI3 4345125 GK3R96-UI1 548098 GK3R97-UI2 5292136 GK3R98-UI3 3708501 At http://genomics-lab.fleming.gr/fleming/GKlab/run340/metaseqr_quantseq_run340/index.html you will find the metaseqR [1] differential gene expression analysis using the contrasts "UI_vs_TI","UI_vs_GIH","UI_vs_GIL","TI_vs_GIH","TI_vs_GIL","GIH_vs_GIL" (note the used naming convention: in A_vs_B, A is always the reference). The sample GIH2 has an unusual length distribution (see http://genomics-lab.fleming.gr/fleming/GKlab/run340/Auto_user_IONAS-340-GKlab_170327_GK3R87-98_439.pdf) and it clusters together with the TI samples. For these reasons, a differential gene expression analysis using without the sample GIH2 is at At http://genomics-lab.fleming.gr/fleming/GKlab/run340/metaseqr_quantseq_run340_without_GIH2/index.html Best wishes and happy Easter, Martin [1] Moulos P and Hatzis P “Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns.” Nucl. Acids Res. (2014) doi: 10.1093/nar/gku1273 http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract. #@ Dear Panagiotis, thanks again for your support, one group was delivered yesterday. In the next, a strange phenomenon occurrs. The analysis with all samples worked fine: samplename filename condition paired stranded GK3R87-GIH1 /data/images/proton/run340/www/GK3R87-GIH1.bam GIH single yes GK3R88-GIH2 /data/images/proton/run340/www/GK3R88-GIH2.bam GIH single yes GK3R89-GIH3 /data/images/proton/run340/www/GK3R89-GIH3.bam GIH single yes GK3R90-GIL1 /data/images/proton/run340/www/GK3R90-GIL1.bam GIL single yes GK3R91-GIL2 /data/images/proton/run340/www/GK3R91-GIL2.bam GIL single yes GK3R92-GIL3 /data/images/proton/run340/www/GK3R92-GIL3.bam GIL single yes GK3R93-TI1 /data/images/proton/run340/www/GK3R93-TI1.bam TI single yes GK3R94-TI2 /data/images/proton/run340/www/GK3R94-TI2.bam TI single yes GK3R95-TI3 /data/images/proton/run340/www/GK3R95-TI3.bam TI single yes GK3R96-UI1 /data/images/proton/run340/www/GK3R96-UI1.bam UI single yes GK3R97-UI2 /data/images/proton/run340/www/GK3R97-UI2.bam UI single yes GK3R98-UI3 /data/images/proton/run340/www/GK3R98-UI3.bam UI single yes As one sample (GIH2) has strange length distribution, I rerun without this sample and get: " Plotting meandiff...Error in files$meandiff[[n]] <- unlist(fil[[n]]) : more elements supplied than there are to replace " Best wishes, Martin