Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 24

Systematic literature review question doubt

There are as of now quite a decent number of R library to run meta-analysis. This paper is one of the many which i have seen. Now...

Asked on 05/16/2021

0 answer

How do I create Protein Ligand images

I was wondering how I can create images showing the bonds and the residue codes involved in the bound Protein Ligand complex obtained after Molecular Docking as depicted in the...

Asked on 05/15/2021

3 answer

Is there public RESTful api for Gnomad?

I currently find Harvard's RESTful API for ExAC extremely useful and I was hoping that a similar resource is available for Gnomad? Does anyone know of...

Asked on 05/14/2021 by Pasted

5 answer

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go...

Asked on 05/13/2021 by Jabbath

1 answer

TopHat2 versus HISAT2 inner workings

In my intro to bioinformatics course, we mentioned that TopHat2 and HISAT2 will both try to align as many reads as possible to the reference genome (TopHat2 has been superseded...

Asked on 05/11/2021

1 answer

Question of Padj value (very high, infinite) got from dds

After I got dds from my count matrix by DESeq(), I use results() method to get Padj and log2 fold changes for volcano plotting,then I found some gene's Padj...

Asked on 05/10/2021

1 answer

nextflow: Filter outputs of a process

How could I filter outputs of a process in the input of the next process? Filtering works fine in channel, but if I try to filter outputs I got compilation...

Asked on 05/10/2021 by zillur rahman

1 answer

Gene expression Table to Expression Matrix converstion

I have an RNAseq gene expression file (Count data) as follows, I need to conduct a Differential gene expression analysis between Patients, for that, I need to have this file...

Asked on 05/10/2021

1 answer

Filtering VEP annotation file

I am filtering a VEP annotated vcf, trying to maintain just those variants classified as deleterious by SIFTand as damaging (probably or possibly included) by PolyPhen. I am using:filter_vep...

Asked on 05/10/2021 by Jeni

1 answer

Find common SNPs in multiple VCF files

I have 3 VCF files.A1.vcfA2.vcfA3.vcfI want to get the common SNPs that are present in all these three files. And output must be in vcf format. output:common_A.vcf...

Asked on 05/09/2021

1 answer

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