User: jordi.planells

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Posts by jordi.planells

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Answer: A: How to map reads onto human hg38 gene body regions instead of whole genome?
... I would get the fasta file of the human transcripts and map it against it. You can get the RefSeq annotation from [here][1]. Then you can build an index with your favorite aligner and align against it. Other option would be to extract the genes from a gtf annotation and use ```bedtools getfasta `` ...
written 4 days ago by jordi.planells330
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Comment: C: Interpretation of PCA plot
... Look at other PCs. In this plot you are representing PC1 and PC2. You could instead represent PCs 3,4, etc. It looks that the day the different samples were processed is not affecting your analysis. However, I would do the same plot with cell type instead to be entirely sure. ...
written 5 weeks ago by jordi.planells330
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Comment: C: Interpretation of PCA plot
... What you see here in the PCA plot is how similar (or different) your samples are. You should question yourself whether your samples are clustered by batch or by biological semblance. If the clustering you see has sense biologically, then you can proceed with the analysis, otherwise you should do a ...
written 5 weeks ago by jordi.planells330
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Comment: C: No coverage in macs2 peak summit!
... Inconsistent annotations? Are both the same release, same source? ...
written 5 weeks ago by jordi.planells330
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Comment: C: Principle component analysis
... You can set the cutoff you like, `0.8` was just a random number I used for the example. The cutoff you are applying is arbitrary so you decide which is the threshold you want to use. ...
written 5 weeks ago by jordi.planells330
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Comment: C: Principle component ananlysis
... you can slice featureCos2 or featureContrib as a regular dataframe. Example: `df[df$X>0.8,]` In the example above, you are selecting the rows of `df` that have a value greater than 0.8 in the column X. Also try to format your question, using the `code` typography. Try to have each line of c ...
written 6 weeks ago by jordi.planells330
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Comment: C: DESeq2 discrepancy between analysis.
... My samples cluster totally independent long and short fraction in a PCA, that's why I was wondering whether I have a situation as the one mentioned in the vignette... See the plot [here][1] [1]: https://ibb.co/K5ZRqQR ...
written 6 weeks ago by jordi.planells330
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DESeq2 discrepancy between analysis.
... Hi all! I am writing to you because I need help/advice on a DESEq2 analysis that I'm performing. I have 4 different knockdowns (A,B,C,D) and 2 different chromatin fractions (short, long). I want to compare results within each chromatin fraction, let's say A is my mock KD, so B,C,D vs A in long fr ...
R deseq2 rna-seq written 6 weeks ago by jordi.planells330 • updated 6 weeks ago by swbarnes29.3k
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Comment: C: can't install cummeRbund
... See [this][1] post. Then you can try to reinstall the problematic packages. [1]: https://askubuntu.com/questions/1254106/updating-r-3-5-3-to-r-4-0-2-on-ubuntu-18-04 ...
written 6 weeks ago by jordi.planells330
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Comment: C: can't install cummeRbund
... `ERROR: configuration failed for package ‘XML’` Seems that this package couldn't be installed. Try to install it and to pay attention to the error log. You will probably be missing some ubuntu libraries. When you detect the missing library, then google the name and see how to install it (almost su ...
written 6 weeks ago by jordi.planells330

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Using forloop to add headers to multiple files
Scholar 6 months ago, created an answer that has been accepted. For A: One sample Wilcoxon test for each boxplot ggplot2
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: One sample Wilcoxon test for each boxplot ggplot2
Scholar 6 months ago, created an answer that has been accepted. For A: One sample Wilcoxon test for each boxplot ggplot2
Epic Question 13 months ago, created a question with more than 10,000 views. For geom_bar plot with several variables
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