User: Radek

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Radek840
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840
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Belgium
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6 minutes ago
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2 years, 1 month ago
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Posts by Radek

<prev • 100 results • page 1 of 10 • next >
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Comment: C: No differential gene expression after tuxedo protocol
... If you see the mapping of the reads (with IGV for example) and bedtools is not working you could use [featureCounts][1]. If I had to use DESeq2 from scratch I would start there [Bioconductor: Differential expression][2]. It also includes a guide to create your matrix of count. [1]: http://bi ...
written 1 hour ago by Radek840
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Comment: C: No differential gene expression after tuxedo protocol
... More up to date differential expression pipeline exist (DESeq2, limma-voom, kalisto+sleut, etc). When you say you have 4 different samples do you mean 4 different conditions you want to compare with one sample in each or 4 samples per conditions? ...
written 3 hours ago by Radek840
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Answer: A: how to using STAR ?
... No you can't. STAR is not designed for DNA but RNA sequencing. [STAR: ultrafast universal **RNA-seq** aligner][1] Use something like bwa, bowtie2 or bbmap. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/ ...
written 28 days ago by Radek840
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Answer: A: counting the reads mapped only to the coding sequence
... Did you look at this answer? [Question: htseq counts on genes (introns + exons)][1] [1]: https://www.biostars.org/p/221422/ ...
written 5 weeks ago by Radek840
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karyoploteR: custom genome axis $latest.plot
... Hi! I would like to dynamically modify the axis from custom genomes plotted with karyoploteR. Example: library(karyoploteR) custom.genome <- toGRanges(data.frame(chr="chr1", start=1, end=10e7) kp <- plotKaryotype(genome = custom.genome) regions <- GRanges(seqnames=rep(" ...
R karyoploter written 5 weeks ago by Radek840
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Comment: C: Enrichment of genomic feature in DNA breakpoints
... For an enrichment you should indeed used "greater" ...
written 7 weeks ago by Radek840
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(Closed) WTSI Mutational Signature Framework: matlabpool function
... Hi! I am trying to use ***WTSI Mutational Signature Framework*** from Alexandrov L. to deconstruct some mutation patterns. http://nl.mathworks.com/matlabcentral/fileexchange/38724-wtsi-mutational-signature-framework Unfortunately I am not familiar at all with matlab. I got from my university a ve ...
matlabpool wtsi matlab written 9 weeks ago by Radek840
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Comment: C: RNA-Seq in Bioconductor
... Have you red the DESeq2 manual? It is full of examples at the end. Each of them can be downloaded through R. ...
written 9 weeks ago by Radek840
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Comment: C: R loop not functional
... I am not sure I understand what you want to do. Is it "if your value(gene X) is comprised between value(gene A) +/- 0.3 you print something like 'TRUE' if not 'FALSE' " ? If so it would be either to go for a statement like the following one: if(b < a+0.3 | b > a-0.3) print(TRUE) else { print ...
written 9 weeks ago by Radek840
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Answer: C: RNA seq data analyses
... Have thought about using a differential expression analysis? Using a program such as DESeq2/edgeR/Limma to compare your tissues with or without treatment ( ~ alcohol_treatment) and your cells with or without treatment ( ~ alcohol_treatment) separately. Then looking in those two analysis which gene ...
written 11 weeks ago by Radek840

Latest awards to Radek

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
Appreciated 3 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For C: Is going back to the wet lab worth it?
Appreciated 7 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 11 months ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots
Supporter 11 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 2.1 years ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots

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