Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 19

install bowtie2 from sources cannot find -ltbb

I am trying to install bowtie2 aligner from sources without the root access.Bowtie2 needs tbb package to be installed and it is recommended to install oneTBB.# install one...

Asked on 06/25/2021 by Suvar

1 answer

Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp) - almost 100 samples altogether. I have to use the...

Asked on 06/25/2021

5 answer

Tool for rna/lna melting temperature prediction

Is there any tool available to predict the melting temperature for rna/lna oligos with its perfect complement ? I know this amazing website from qiagen/geneglobe that estimates the tm...

Asked on 06/24/2021

1 answer

Getting Unique Identifier List for GEO Datasets NCBI

AIM: Download "Unique Identifier List" for the following query from GEO DataSets. Query: ("Expression profiling by high throughput sequencing"[DataSet Type] AND ("Homo sapiens"[Organism] OR "Mus musculus"[Organism] OR...

Asked on 06/24/2021 by Pawan Verma

2 answer

MSA (protein) with biopython or something else?

I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using...

Asked on 06/24/2021 by CuriousTree

1 answer

Problem with merge data while trying to convert gene names in R

This question has also been asked on Biostars and StackOverflow I've been trying to code (in R) a way to convert gene accession numbers to gene...

Asked on 06/23/2021 by Equinox

2 answer

How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I...

Asked on 06/22/2021

0 answer

Is there any value in scaffolding the output contigs of MEGAHIT assembler given a metagenomic dataset?

As far as I understood, for most assembly programs, the scaffolding step takes into consideration paired-end information in order to get from contigs (contiguous sequences) to scaffolds (longer sequences that...

Asked on 06/21/2021

2 answer

How to tell if our ligand-protein docking is good from AutoDock Vina's result

I have perform a ligand-protein docking using Autodock Vina.The result of the docking looks like this:WARNING: The search space volume > 27000 Angstrom^3 (See FAQ)Detected...

Asked on 06/20/2021 by scamander

1 answer

Survival analysis using CoxPH - Effect of covariates

Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package.According to the documentation, the function plot_partial_effects_on_outcome() plots...

Asked on 06/17/2021 by beerzy

1 answer

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