User: prasundutta87

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prasundutta87360
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Posts by prasundutta87

<prev • 170 results • page 1 of 17 • next >
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Comment: C: methylation % calculation for targeted region
... Hi, Thanks for your reply. I just wanted to get methylation % as of now..but I have got a reply now..you can go to this link to find the answer, was meaning to post it anyway here: https://github.com/FelixKrueger/Bismark/issues/354 ...
written 18 days ago by prasundutta87360
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Comment: C: methylation % calculation for targeted region
... Cross-posting in main GitHub for bismark page, hopefully, will get a reply there. ...
written 20 days ago by prasundutta87360
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methylation % calculation for targeted region
... Hi, I want to get the **average methylation % for a targeted region**, for example, see below... Chrom start end Meth_% count_methylated count _unmethylated chr1 1371409 1371409 0 0 5 chr1 1371539 1371539 0 0 88 chr1 1371567 1371567 2.32 2 ...
methylation written 20 days ago by prasundutta87360
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Comment: C: EPIC methylation manifest GRch38 query
... Found the answer myself, it turns out that its 0-based, however, when pasted in UCSC genome browser, 3 nucleotides come up, but that's because the browser runs on the 1-based coordinate system. ...
written 26 days ago by prasundutta87360
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EPIC methylation manifest GRch38 query
... Hi, The new Infinium MethylationEPIC v1.0 B5 Array Manifest File that was released in March 2020 (https://emea.support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html), finally has the start and end positions for hg38 genome for each probe. For example, for one pr ...
epic bedgraph coordinates methylation cpg written 28 days ago by prasundutta87360
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Comment: C: Is plotMDS (from limma package) a PCA (Principal Component Analysis) or a PCoA (
... [This video][1] may be helpful for a basic understanding on this topic. [1]: https://www.youtube.com/watch?v=GEn-_dAyYME& ...
written 4 weeks ago by prasundutta87360 • updated 4 weeks ago by ATpoint36k
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Comment: C: query regarding using manifest and annotation in Minfi (EPIC Methylation array a
... Posting directly to Minfi GitHub page.. ...
written 8 weeks ago by prasundutta87360
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query regarding using manifest and annotation in Minfi (EPIC Methylation array analysis)
... Hi, I am analyzing some samples that were analyzed for methylation sites on an EPIC Methylation array (https://emea.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html). I am trying to analyze it using the latest version of the Minfi package in R. I have a basic question ...
R epic array minfi methylation written 8 weeks ago by prasundutta87360
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Comment: C: array jobs accessing one binary in population genetics software
... Thanks @ATpoint..that's reassuring..the program is in generally quite slow and also hogs a lot of memory..was trying to see if the binary access is a bottleneck that can be avoided..had also thought of making multiple copies of the binary and then use it for each population.. ...
written 3 months ago by prasundutta87360
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array jobs accessing one binary in population genetics software
... Hi, I am trying to run the program SNeP (https://sourceforge.net/projects/snepnetrends/files/binaries/). I have the binary installed in my home directory of the SGE cluster I am using. I wish to run multiple instances of the program for different sets of populations. I have 10 different populations ...
software sge population genetics written 3 months ago by prasundutta87360 • updated 3 months ago by ATpoint36k

Latest awards to prasundutta87

Popular Question 9 days ago, created a question with more than 1,000 views. For strand bias filter for strand specific RNAseq data variants
Popular Question 5 weeks ago, created a question with more than 1,000 views. For strand bias filter for strand specific RNAseq data variants
Popular Question 5 weeks ago, created a question with more than 1,000 views. For variant annotation issue
Popular Question 3 months ago, created a question with more than 1,000 views. For PCA implementation in plink
Popular Question 4 months ago, created a question with more than 1,000 views. For Correct way to report variant statistics from bcftools stats report
Popular Question 5 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 7 months ago, created a question with more than 1,000 views. For PCA implementation in plink
Popular Question 8 months ago, created a question with more than 1,000 views. For PCA implementation in plink
Popular Question 8 months ago, created a question with more than 1,000 views. For fastqc adapter content
Popular Question 9 months ago, created a question with more than 1,000 views. For fastqc adapter content
Popular Question 10 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Student 10 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 11 months ago, created a question with more than 1,000 views. For HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
Popular Question 16 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 18 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Popular Question 19 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 19 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Student 21 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 21 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 22 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 23 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 2.0 years ago, created 100 posts.
Supporter 2.2 years ago, voted at least 25 times.
Scholar 2.9 years ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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