User: baxy

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baxy150
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Posts by baxy

<prev • 23 results • page 1 of 3 • next >
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Confused with epistasis...
... Hi, I want to count epistatic interactions inside human genome. [BioGrid][1] provides a list of genetic and protein interactions. Is it ok to assume that those interactions can be viewed as epistatic? I am asking around but it seams everyone has its own undetermined oppinioun on this matter. Can ...
genome written 9 months ago by baxy150 • updated 9 months ago by Jean-Karim Heriche24k
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Convert BCF2 to BCF1 for legacy pipelines
... Hi, Is there a way to convert BCF2 to BCF1 format in order to comply with legacy pipelines built on top of samtools-0.1.19 Thnx ...
vcf samtools sequencing written 3.0 years ago by baxy150
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Comment: C: perl script to generate the fastq file
... https://www.biostars.org/p/2194/ https://omictools.com/read-simulators-category perhaps?? ...
written 3.2 years ago by baxy150
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News: Bioinformatics, Statistics and R for Next Generation Sequencing Data Analysis
... Hi, If anyone is interested there are two courses being organized in Croatia on the topic of Bioinformatics and NGS analysis. More info available at: [www.exaltum.eu/courses/December2017/][1] Sorry if I've posted this in a wrong place. Please relocate or remove if inappropriate Thank you ...
news next-gen sequencing written 3.2 years ago by baxy150
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Fst computation utilizing epigenetic modifications like histon modifications or methylation
... Hi, can anybody give some advice on how to compute Fst values between populations given a set of epigenetic modifications associated to those populations. Let say I have the information on what is methylated in my genome in 4 populations (2 controls and 2 exposed to something that causes epigeneti ...
populatio sequencing methylation ngs fst written 3.6 years ago by baxy150
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dnds computation suggestions requiried
... Hi I would like to compute dn/ds ratio for each gene in my genome and I am looking for a conceptual protocol on how to do it and which tools to use. For example: First i need to find a homologue (ortholog ? ) to my gene in species A. In this case would it be better to simply take the closest speci ...
genome alignment written 3.7 years ago by baxy150
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What ought to be the rate between methylated CpGs and CHX in RRBS ?
... Hi the question is quite straight forward. I used bismark to map my reads and compute ratios between the total number of methylated C's in CpG context and methylated C's in CHH context. I did the same for unmethylated and got that my ratios are 1:(6-12) (methylated C's in CpG context : methylate ...
next-gen snp written 3.7 years ago by baxy150
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Forum: What is the current price of a bioinfo group?
... General idea: **To set up a small competitive bioinformatic group consisting of 3 bioinformatitions.** Questions: 0. What is the basic requirement of one such group ? (for example: working space, a chair, a desk, a computer, etc.) 1. What kind of a software it requires? 2. What would be the ...
bioinformatics forum written 3.8 years ago by baxy150
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Minor allele frequency - homoplasmy and heteroplasmy
... Hi, Could anyone help clarify these concepts? 1. MAF refers to minor allele frequency, right? so given 10 ppl if there are 3 alleles, with frequencies of 0.50 (G), 0.4 (A), and 0.1(C) MAF is 0.4, right? which means 4 ppl have A? 2. In case of mtDNA the above case would refer to what exactly? So ...
next-gen snp written 4.0 years ago by baxy150
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Forum: Publishing and research fees
... Hi, I have a quick question. For a while now I am working outside academic circles and unable to get back in (to tell the truth did not try too hard, I like non-academic lifestyle, at least the illusion of freedom feels a bit more real ;)). However, I am still working independently in my free tim ...
publishing forum research funding written 4.1 years ago by baxy150 • updated 4.1 years ago by Chirag Nepal2.3k

Latest awards to baxy

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Bioinformatics, Statistics and R for Next Generation Sequencing Data Analysis
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Minor allele frequency - homoplasmy and heteroplasmy
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Ensembl Perl API
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Remove Fasta Sequences with Duplicate IDs (but with different Descriptions) & Ap

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