Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 18

Extracting WDL map keys as a task

I want to get the array of keys from a map data structure, so I can perform array-based functions against the map in subsequent tasks. I am limited to draft-2...

Asked on 07/05/2021 by Xophmeister

1 answer

How to activate an installed plugin (NetworkAnalyzer) on Cytoscape?

I need to use NetworkAnalyzer to analyse the nodes of a PPI network on Cytoscape, but the pre-installed app is not displayed on the Tools menu. I checked the App...

Asked on 07/04/2021

0 answer

Reliably create female and male individuals in a -ped file for plink

For a study I need some kind of "decoy" GWAS-data. For this I created a panel with some genes, the same ones as in the real data. From NCBI I...

Asked on 07/04/2021

0 answer

RNASeq analysis using featureCount and EdgeR

I am using a pipeline (bam -> featurecount-> EdgeR) to do some RNASeq analysis of several groups and sub-groups. For example, I have the following dataset with two types (T1...

Asked on 07/04/2021

1 answer

A database for RefSeq protein accession IDs

Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein...

Asked on 07/03/2021 by Ehsan Salehabadi

1 answer

two aligners combined results

I would like to ask if someone uses two different aligners to produce count matrices and then run the same alogrithm for DEG analysis, would it make sense to find...

Asked on 07/02/2021

1 answer

How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?

On GISAID they classified the coronavirus using 4 clades(S, G, V, Other).I downloaded around 1,000 complete genomes of the coronavirus from GISAID and...

Asked on 07/01/2021 by yuval

2 answer

Does NCBI's blast API block my IP?

I am trying to run a blatn command from both my laptop and within a google colab notebook. I am not sure why, but this command runs properly once and...

Asked on 07/01/2021

1 answer

What is the fastest way to get the reverse complement of a DNA sequence in python?

I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that...

Asked on 06/26/2021 by conchoecia

8 answer

e-utilities install file seems to be corrupted

I am trying to install e-utilities from the NCBI from this link. When I download the file source ./install-edirect.sh. This successfully installs the e-utilities, except I also...

Asked on 06/26/2021

0 answer

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