User: firatuyulur

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firatuyulur120
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Posts by firatuyulur

<prev • 24 results • page 1 of 3 • next >
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Answer: A: Threshold of removing genes with low counts ?
... I do not think there is a certain threshold. When it comes to drawing a plot out of counts, the zero lines do make your computer suffer as there will be a couple of thousand 0 lines that I remove them directly. While analyzing, you will use differential expression, and there will be a p-value / p.ad ...
written 15 days ago by firatuyulur120
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Comment: C: How to plot a heat map for the top 30 differentially expressed genes.
... many plots automatically order the data alphabetically although you order them in a specific way. to save yourself from this you can first order your data the way you want. then try `my_data$ens_id <- factor(my_data$ens_id, levels = my_data$ens_id)` and then plot. ...
written 15 days ago by firatuyulur120
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Comment: C: Widening the distances between PCA vectors in PCA a biplot
... you could remove the black dot labels with `fviz_pca_biplot(res.pca, label ="var")` or you can simply get rid of black dots with `fviz_pca_biplot(res.pca, invisible ="ind")`. once you remove black dots, if you use xlim and ylim that only encircles your blue arrows. say your arrows are within the x a ...
written 15 days ago by firatuyulur120
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finding unique mutations from a multi-sample VCF
... Hi all, I have gone through many posts and couldnt find my answer. I have a vcf file of 4 samples. What I want to reach from it is the list of unique mutations among samples. Example, at position N their genotypes are as ; 0/1 0/0 0/0 0/0. In such case, this is a unique mutation for sample1 at p ...
vcf snp written 6 weeks ago by firatuyulur120 • updated 6 weeks ago by Pierre Lindenbaum94k
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Answer: A: I am a student, what can i do with 23andme raw data?
... You can check the meaning of each SNP, given with the rs code. There are plenty snp databases where you can detailly read about the effects of each snp. ...
written 9 weeks ago by firatuyulur120
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Answer: A: Plus and minus strands plotted together
... For the ones who have suffered from the same problem; Apparently, GRO-Seq figure is independent of the tool. It is possible to get a visualization as in the link above with any browser. I used [Homer][1] for GRO-Seq analysis. The trick is, when it comes to generating the bedgraph using makeUCSCfile ...
written 10 weeks ago by firatuyulur120
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Plus and minus strands plotted together
... Hi all, I am working on a GRO-Seq data and I want to plot a graph like [one these figures][1], plus and minus strands are reversely merged on the same line. I know that UCSC genome browser can handle this, but in many ways, it becomes user-UNfriendly. So does anyone know a tool or GUI which can plot ...
gro-seq figure chip-seq written 11 weeks ago by firatuyulur120
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Comment: C: multiple SRR in a particular FTP conflict
... yes, thats helpful but the thing is 8million spots for a chipseq data is kind of a low. Should I process them separately and then merge them? or merge the fastqs? I agree that there are 3 runs but not sure whether they are replicates, the three seem to be complementary ? ...
written 3 months ago by firatuyulur120
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multiple SRR in a particular FTP conflict
... Hi all, It might be a silly question but I need to understand this. I am working on some ChIP-Seq data and while I was downloading the SRA from geo, when I [clicked on ftp at very bottom][1] there are [multiple SRR coded folders][2], each holding an SRA file inside. The question is, there is only on ...
chip-seq written 3 months ago by firatuyulur120 • updated 3 months ago by EagleEye3.8k
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rMATS readlength difference
... Hi all, I am trying to work with rMATS to analyse splicing events. With the new version of rMATS, they started using STAR and it does not allow using fastq's with different read length. My fastq read lengths vary between 41 to 50. [Here is the link][1] for one of my fastqc results, which actually re ...
rmats splicing rna-seq written 3 months ago by firatuyulur120

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Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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