Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 45

How to identify to each scaffold a read belongs to, inside a .sam file?

I have a fasta file assembly and combining it with the raw reads we produced a .bam file which I converted to .sam . The .sam information lines look like...

Asked on 11/05/2020 by fullmooninu

1 answer

are GSEA and other geneset enrichment analysis supposed to yield extremely different results between them?

I have recently ran in R four geneset enrichment analysis in the same database (TCGA:breast cancer) comparing two intrinsic subtypes. The methods I used were:MIGSA, that imports mGSZ package and...

Asked on 11/05/2020 by Darío Rocha

1 answer

Meta-analysis and data curation tools in R

I'm looking to run meta analysis. First step is data curation. How exactly data curation for metanalysis is done? I did a few searches which gave me some lead how...

Asked on 11/04/2020

0 answer

Viral Metagenomics

I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray for de novo viral genome assembly before but I haven't done...

Asked on 11/01/2020 by L R Joshi

1 answer

Issues with AutoDock Vina

I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve...

Asked on 10/18/2020 by ibio_rep1

0 answer

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai...

Asked on 10/17/2020

1 answer

Plotting distance tree from blastn output

I'm trying to plot a simple distance tree of my blastn output with nj (like the tree view on NCBI). From what I understood, what I think I should do...

Asked on 10/11/2020

1 answer

Swapping to effect increasing allele in case/control studies

I want to find the effect-increasing allele for a given set of SNPs. For quantitive traits, I understand the effect sign is changed when the A1 and A2 are...

Asked on 10/09/2020 by Dale Handley

0 answer

Error When Using biocLite as an installer in rpy2 python library

I am running into an error when I tried to run the following lines of code, the error at line 3:1 from rpy2.robjects.packages import importr2 base = importr('base')3 base.source("http://www.bioconductor.org/biocLite.R")4...

Asked on 09/27/2020 by aBiologist

1 answer

Why doesn't an (Entrez eutils) einfo request for "gene" return the link gene_nucleotide or gene_nucleotide_pos links?

I'm updating a galaxy tool wrapper for Entrez's eutils suite and I'm trying to create a form with valid link selections (among other things) based on the "from" & "to"...

Asked on 09/10/2020 by hepcat72

1 answer

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