Moderator: venu

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venu5.7k
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Posts by venu

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Comment: C: What can be done to separate the healthy and patient samples in PCA plot and Dis
... > Before going for DESeq2 analysis Does this mean you are directly using raw counts for clustering and PCA? If so, your results are not unusual. Also from the heatmap scale, I really think there is some sort of problem with normalization. You can use DESeq2 rlog/vst normalized counts for PCA. ...
written 20 hours ago by venu5.7k
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Answer: C: Finding and changing a given position in hg19 ref fasta file
... before you start writing all that code, check out [maskfasta from bedtools][1]. Isn't this what you want? [1]: https://bedtools.readthedocs.io/en/latest/content/tools/maskfasta.html ...
written 27 days ago by venu5.7k
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Comment: C: BedtoBam error: Why is this?
... Are you sure `-g` expects `fasta`? If I remember correct it only requires chromosome sizes file in 2 columns. ...
written 5 weeks ago by venu5.7k
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Comment: C: Plot normalized counts DESeq or TPM?
... In an ideal case (any case?), your differential genes from DESeq2 should show same pattern when you plot a box/violin plot with TPMs. Meaning, over expressed genes should show high TPMs and vice versa. But I would once check the clustering heatmap produced by VST counts and TPMs. If the clusters ar ...
written 9 weeks ago by venu5.7k
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Comment: C: Calculate Tag density
... May be you have to look up definition of tag count one more time. Check this: [ChIP seq basic terminology: what is a ChIP-seq tag?][1] > plot the tag density for a certain group of genes What do you mean by plotting? If you want to visualise ChIP enrichment over some genes, you can use `IGV` o ...
written 9 weeks ago by venu5.7k
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Comment: C: Calculate Tag density
... The details are not sufficient to suggest a workflow or tool. You could try to explain in detail what your goal is. That being said, if you have a bed file with gene coordinates and BAM file, there are number of tools to calculate raw read/tag density and normalized read density. E.g. `deeptools`, ...
written 9 weeks ago by venu5.7k
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Comment: C: plot with ggplot2
... Can you show `head(df1`) & `head(df2)`? Seems like you can add add one more column to each `data.frame` e.g. df1$SOURCE <- "df1" df2$SOURCE <- "df2" model_3 = rbind(df1, df2) .... Then color based on `SOURCE` ...
written 10 weeks ago by venu5.7k
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Comment: C: NMF not working for identifying mutational signature
... > I am not able to compare my mutational catalogue with COSMIC 30. And that is exactly what I'd like to do. If that is what all you want to do, check YAPSA package. It has functions to calculate exposures for known COSMIC signatures. You can also specify cut-offs e.g. a signature must be reporte ...
written 11 weeks ago by venu5.7k
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Answer: C: NMF not working for identifying mutational signature
... Sorry to disappoint you but it's not that simple. NMF is a good approach for mutational signatures but where did you see that approach/tutorial? You need a reference set of signatures (COSMIC 30 or PCAWG 60, google it) and a mutational catalogue (the matrix you have now). There are several establi ...
written 11 weeks ago by venu5.7k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... Thanks. I will definitely check the log2 normalized counts. ...
written 3 months ago by venu5.7k

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