User: Radek
Radek • 840
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Posts by Radek
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... 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
Radek • 840
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... 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
Radek • 840
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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
Radek • 840
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... 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
Radek • 840
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... 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(" ...
written 5 weeks ago by
Radek • 840
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... For an enrichment you should indeed used "greater" ...
written 7 weeks ago by
Radek • 840
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... 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 ...
written 9 weeks ago by
Radek • 840
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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
Radek • 840
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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
Radek • 840
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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
Radek • 840
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For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
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