Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 40

if I know the number of sequencing circles can I give this information to DESeq2?

I am trying to understand library normalization in DESeq2. I would like to ask the following: I know that some samples have been run 15 cycles and some others 20,...

Asked on 01/02/2021 by marilu

1 answer

DNA sequence error annotation

Suppose I generate a DNA sequence of the following pattern. AAGTC And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence AAAGGC Where...

Asked on 12/30/2020 by Matthew Jones

0 answer

Program to make a haplotype network for a specific gene

Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. Example:...

Asked on 12/30/2020 by Ryan Fahy

1 answer

Cobratoolbox unable to identify gurobi solver when passing initCobraToolbox

I am running into this issue lately when I am trying to install the Cobratoolbox on matlab along with having installed the prerequisite gurobi solver and adding it to the...

Asked on 12/29/2020

0 answer

How to interpret Mendelian randomization results?

I did Mendelian randomization using this software:https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdflibrary(MendelianRandomization)f=read.table("246LDout272Biobank_Retina.txt", header=T)> head(f) rs exposure.beta exposure.se outcome.beta outcome.se1 rs1029830...

Asked on 12/29/2020 by anamaria

1 answer

Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?

I'am comparing bats coronavirus with Sars2, i.e. COVID-19. I have one question...one Bat Sars coronaviurs identify in GenBank as DQ071615.1 has the ORF13(28122..28415) and ORF14(28572..28784) proteinsSars2 identify in GenBank as...

Asked on 12/26/2020

1 answer

samtools / bamUtil | Meaning of as Reference Name

I have been working with several tools on bam files recently and I am not sure how I should interpret some of the outputs.samtools idxstats mapped.sorted.bamChr1 ...

Asked on 12/25/2020 by Paul Endymion

1 answer

Help Adjusting Bedtools Output in R

I have been asked to write a script in R to edit, using data.frame, this .fa file that is the result from extracting gene sequences from a repeat masker coordinate...

Asked on 12/23/2020

1 answer

How to remove batch effect from TCGA and GTEx data

I want to play some differentially expressed genes for gliomas cancer. I collected cancer tissue profiles from the TCGA database and normal tissue profiles from the GTEx database. I straightforward...

Asked on 12/22/2020 by Kai He

2 answer

Blast templates not found in PSI-TM Coffee

I'm trying to run psicoffe mode on Ubuntu 18.04, but it returns the error: 17633 -- WARNING:Impossible to find BLAST TemplatesCheck that your blast server is properly installed...

Asked on 12/22/2020 by Poccia

0 answer

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