User: mark.pekarsky

gravatar for mark.pekarsky
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4 months ago
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4 months, 3 weeks ago
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m************@yandex.ru

Posts by mark.pekarsky

<prev • 5 results • page 1 of 1 • next >
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DESeq2 analysis of two tissues with 3 different conditions
... Hi, these are my very first steps in RNAseq and for the first time in my life I am trying to use a DESeq2 package in R, and I am trying to figure out how can I "sort" my results if I have **two tissues** (**intestine and brain**) and for each tissue I have **3 conditions - "control", "black" and "wh ...
R deseq2 rna-seq written 4 months ago by mark.pekarsky20 • updated 4 months ago by swbarnes27.5k
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Invalid covariate name
... Hi, I am trying to follow this ballgown tutorial https://rpubs.com/selveyad/ballgown_tutorial I do create two ballgown objects, e.g. bg = ballgown(dataDir = "ballgown", samplePattern = "HI.3923.001.Index", pData = phenodata ) and bg_filt = subset(bg, "rowVars(texpr(bg)) >1", genomesub ...
R ballgown rna-seq written 4 months ago by mark.pekarsky20 • updated 4 months ago by Biostar ♦♦ 20
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Answer: A: Cannot run stringtie
... I have the answer now - it was all due to the version, I needed to use the v1.3.4 release. The problem is solved now. Thanks to all contributors. ...
written 4 months ago by mark.pekarsky20
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Comment: C: Cannot run stringtie
... Lmod is automatically replacing "intel/2016.4" with "gcc/5.4.0". Due to MODULEPATH changes, the following have been reloaded: 1) openmpi/2.1.1 Due to MODULEPATH changes, the following have been reloaded: 1) openmpi/2.1.1 The following have been re ...
written 4 months ago by mark.pekarsky20
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Cannot run stringtie
... Hi, I am new to bioinformatics so I am trying now to complete an RNAseq procedure descriped in the famoust Salzberg paper.. I am using a cluster to run all these programs so I just load modules... I am on a stringtie step and when I am trying to run my script I have that kind of error: ------ ...
rna-seq written 4 months ago by mark.pekarsky20

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