User: alexandr.gopanenko

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2 years, 7 months ago
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2 years, 9 months ago
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Posts by alexandr.gopanenko

<prev • 11 results • page 1 of 2 • next >
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What tool for reads alignment are prefereble for wavClusteR input bams?
... Hello everyone! I want to analyze my PAR-CLIP data utilizing wavClusteR. So when I try to create count table from my bam file (prepared by CLC WB) by command below countTable <- getAllSub( Bam, minCov = 10 ) I have the error like that: Error in { :    task 1 failed - "solving row 140: range c ...
wavcluster written 2.6 years ago by alexandr.gopanenko20 • updated 2.6 years ago by federico.comoglio100
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Comment: C: How to extract only mRNA from TxDb object?
... Thank you very much for your advice, it works nice! ) ...
written 2.7 years ago by alexandr.gopanenko20
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How to extract only mRNA from TxDb object?
... Hello everybody!    I want to extract only mRNA from TxdB. So I did the following steps: txdb <- makeTxDbFromGFF("Homo_sapiens.GRCh38.85.gtf", format="gtf" ) exonsByGene <- exonsBy(txdb, by="gene") exonsByGene contains all exons including exons related to non-protein coding genes. The que ...
genomicfeatures written 2.7 years ago by alexandr.gopanenko20 • updated 2.7 years ago by Johannes Rainer1.4k
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Comment: C: How to combine replicates creating heatmap?
... Michael, thank you very much for your advice! ...
written 2.7 years ago by alexandr.gopanenko20
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How to combine replicates creating heatmap?
... Hello! When I do DE analysis of my RNA-seq data I often have 3-4 replicates of each condition. So, I want present heatmap contaning only condition1_vs_condition_2. I realize that it will not contain information about variations between replicates but I think it will be easy for understanding.   ...
edger deseq2 heatmap.2 written 2.7 years ago by alexandr.gopanenko20 • updated 2.7 years ago by Michael Love24k
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Comment: C: Analysis of Ribo-seq with poly(A) mRNA RNA-seq
... Thank you very much! It sounds good )  ...
written 2.7 years ago by alexandr.gopanenko20
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Analysis of Ribo-seq with poly(A) mRNA RNA-seq
... Hello! I want to analyze my ribosome profilig data coupling with RNA-seq (poly(A)) using DESeq2. So, ideally, my data contains only mRNA fragments but it's not true, cause for example Ribo-seq contains a lot of rRNAs, small RNA's that copurified with monosomes ad etc. In RNA-seq only 70-80% mapped ...
genomicfeatures deseq2 genomicalignments written 2.8 years ago by alexandr.gopanenko20 • updated 2.8 years ago by Michael Love24k
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Comment: C: Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work
... Thank you very much! ) I've checked my input data by your method targets$Factor %in% unique(as.character(cmp[[1]]))  and found problems with my targets.txt file. So, some targets.txt file manipulations solved my problem ) ...
written 2.8 years ago by alexandr.gopanenko20
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Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work
... Hello! I have some problems with run_edgeR or run_DESeq2 functions from systempipeR package. I 've done all required steps described in vignette and  when I've tried to do run_edgeR by command: edgeDF <- run_edgeR(countDF = countDF, targets=targets, cmp=cmp[[1]], independent=FALSE, mdsplot="") ...
systempiper run_edger written 2.8 years ago by alexandr.gopanenko20 • updated 2.8 years ago by Thomas Girke1.7k
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Comment: C: How to extract transcripts from Txdb with length >100
... Thank you very much! ...
written 2.8 years ago by alexandr.gopanenko20

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