User: banerjeeshayantan

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Posts by banerjeeshayantan

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Types of base substitutions
... I was reading this Wikipedia article on Mutational Signatures and I came across this section titled **Types of mutations: base substitutions**. I don't understand why the C>A mutations are indistinguishable from G>T. When we are cataloging the mutations we do have the strand information, righ ...
genome snp written 13 days ago by banerjeeshayantan190
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How to run bedtools from inside a python program
... I have been using the bedtools to extract fasta sequences based on genomic positions mentioned in a bed file. The command that I usually use os the following: bedtools getfasta -fi input.fa -bed input.bed -fo out.fa Now I want to implement the same command line from a python program. This i ...
bedtools python commandline written 23 days ago by banerjeeshayantan190 • updated 23 days ago by Joe18k
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Comment: C: Batch effect removal with the help of sva
... Thanks a lot for your help and for providing the links. It's just that I have gone through quite a few papers that have adjusted for batch effects using Combat and used the corrected data for finding DEGs. But after learning about the apparent perils of going down that road, I am pretty sure I won't ...
written 27 days ago by banerjeeshayantan190
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Comment: C: Batch effect removal with the help of sva
... Understood. So basically I wanted to see the before and after plots and check how one can use sva to discover the unwanted variations in your data. However, for obtaining the batch corrected data, I am using Combat and obtaining the cleaned expression matrix outputted by the same. Hope that's ok. ...
written 27 days ago by banerjeeshayantan190
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Comment: C: Batch effect removal with the help of sva
... Thanks a lot for your explanation. The concept is more clear to me now. Basically, find the set of covariates that best explains the variability in the dataset due to batch effect and produce a boxplot of the inferred covariate (sv[,2]) in this case vs the actual effect. Could you also please let me ...
written 27 days ago by banerjeeshayantan190
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Batch effect removal with the help of sva
... I was recently going through the concepts required to remove batch effects from gene expression data. In particular, I was going through [this tutorial][1] by Jeff Leek and trying out the codes mentioned there. From what I have understood from the analysis, SVA is similar to PCA and tries to find tw ...
sva gene expression batch effect written 28 days ago by banerjeeshayantan190 • updated 28 days ago by Papyrus550
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Feature extraction pipeline for CHASMplus
... I am trying to extract the features that were used to train the CHASMplus tool for driver mutation prioritization. Although the list of features is available in the [Supplementary Materials][1], I was wondering if there was a way to extract features for a new set of mutations (Chromosome/Position/Re ...
chasmplus written 8 weeks ago by banerjeeshayantan190
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Comment: C: Convert variant coordinates from one genome build to the other
... Thanks for sharing. Much appreciated. Just to clarify I will get the reference/alternate allele mapping too, right? ...
written 9 weeks ago by banerjeeshayantan190
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Convert variant coordinates from one genome build to the other
... I have a list of variants (Chromosome/Position/Ref/Alt) based on the GrCh38 build of the human genome. To reproduce the results from a paper, I have to map these coordinates to the GrCh37 build of the human genome. Now I understand that the UCSC LiftOver tool maps the coordinates (Chrosome/Position) ...
variant sequence genome_build written 9 weeks ago by banerjeeshayantan190
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Comment: C: Conserved regions around mutations
... I understand your point. Can you tell me a bit more about downloading a "public conservation track for the region"? Where can I find this? ...
written 3 months ago by banerjeeshayantan190

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Popular Question 13 days ago, created a question with more than 1,000 views. For Annotate merged vcfs
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