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Answer: Bedtools intersect 0- and 1-based coordinate files

A: Gene Set Analysis Software That Takes A Vcf As Input

C: deseq2 replicates error

Using VEP to get gnomAD frequencies

Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'?

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Popular Question to J.F.Jiang ▴ 860

Recent Replies

Comment: Bedtools intersect 0- and 1-based coordinate files by maxrwjones898 ▴ 10

Ah wonderful, good to know! Brilliant answer and thanks for the code / outputs to back it up.

Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'? by GenoMax 101k

> clients proprietary sequences which cannot by processed on public > website. No option but to download `nr` indexes and do the search lo…

Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'? by matt ▴ 10

I would like to be able to do ‘blastp’ with clients proprietary sequences which cannot by processed on public website. Until now I did it …

Answer: Bedtools intersect 0- and 1-based coordinate files by ATpoint 49k

> Does bedtools intersect automatically take this difference into account? Yes, it is quite a smart one. Example (BED vs GTF, random file…

Comment: Issue on downloading fastPHASE in Mac by 4galaxy77 ▴ 510

Out of polite curiosity, what use to people have for fastPHASE in 2021? I believe it's still the most accurate method, but pretty slow. So …

Comment: Snakemake and STARsolo by Jeremy Leipzig 20k

one of them is `{sample}.Aligned.out.sam`. Start by creating a target variable that point to the sam files you want produced SAMPLES =…

Comment: T-test analysis for gene expression comparison by bioinformatics2020 ▴ 580

THIS! You need to go back and learn about what type of distribution is used for a t-test. Then start understanding the distributions that g…

Comment: Warning messages: In svgStyleAttributes(style, svgdev) : Removing non-S by xxxxxxxx ▴ 20

arrayQualityMetrics version- 3.47.0

Comment: Liftover vcf file from hs37d5 assembly to b37 assembly by Pierre Lindenbaum 135k

don't you just have to rename the chromosomes (if needed) and discard the chromosomes that are not present in the other reference ?

Answer: How to extract translated sequence of pol gene from a GenBank file by GenoMax 101k

This is a duplicate post of a question already asked here --> https://www.biostars.org/p/9470184 Please use the other post. This post will…

Answer: How to extract translated sequence of a partcular gene by parsing GenBank file by GenoMax 101k

Here is one solution based on [EntrezDirect][1]: $ esearch -db protein -query "Human immunodeficiency virus 1 AND pol [gene]" | efetch…

Comment: Haploview formats by abdin-marwa • 0

This seems pretty helpful. Thank you so much.

Comment: Warning messages: In svgStyleAttributes(style, svgdev) : Removing non-S by 4galaxy77 ▴ 510

what version of arrayQualityMetrics are you using?

Comment: Single cell analysis by najioumayma ▴ 20

Thanks a lot for your help , it's clear for me now.

Answer: Negative Fst values in Lositan by andemexoax • 0

I ran into this using SNPrelate package in R to calculate FST values. The references for the SNPrelate function that computes FST 1. We…

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