Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 41

Genome scaffolding

I have assembled a virus genome using Ray resulting in approximately 5000 contigs. Now I want to build a scaffold of those contigs to get the full...

Asked on 12/22/2020

3 answer

If a gene is expressed at a level of 1/1200 compared to the average gene, how is probability 50:50 that we have a read mapped to it?

I am reading a book about RNAseq analysis and it says"To calculate the probability that a read will map to a specific gene, we can assume an average gene size...

Asked on 12/20/2020 by Bio314

1 answer

Discrepany between AutoDock Vina and AutoDock Tools

I have been calculating the binding Affinity between a Ligand and a Protein using both AutoDock Vina and AutoDock tools but the binding affinity estimates obtained from the 2 molecular...

Asked on 12/20/2020

0 answer

How many single copy gene are needed to construct the phylogenetic tree?

I ran the orthomcl program with genomes of the whole streptomyces genus(from ncbi) as input, but I only got 22 orthologous groups(streptomyces's genome size vary from 2M to 15M, which...

Asked on 12/18/2020 by TANGLi83

1 answer

Time for running ADMIXTURE analysis

I am trying to run the ADMIXTURE software for the first time to analyse the structure of an in-house dataset of samples comparing to 1000 genomes project ancestral populations. I...

Asked on 12/17/2020 by Iriel

1 answer

Output the linear predictor from a stratified cox model?

I have fitted a cox model on a pooled dataset of multiple studies, say study A, B and C. As these studies have different baseline hazard functions, I stratified for...

Asked on 12/17/2020 by Nienke

1 answer

FastQC and Trimmomatic in Galaxy?

I am independently working on data retrieved SRA database, paired-end data as separate inputs. After running FastQC using Galaxy, majority of the modules have failed. I tried Trimmomatic with default...

Asked on 12/16/2020

0 answer

Measure the purifying selection for certain taxa along a phylogeny

I am posting this message because I need clarity about the analysis I want to perform.In my analysis, I have a homologous gene in 13 species, and I would...

Asked on 12/14/2020

1 answer

What type of Protein ID is this?

I got a FASTA file from NCBI RefSeq.These proteins are annotated with IDs like this : protein_id=XP_019970915.1.What type of ID is this? I would like to have them...

Asked on 12/14/2020 by Firingam

1 answer

How to find all WGS assemblies accessions of a species

Some backgroundSimilar to the OP of https://www.biostars.org/p/377840/, I would like to programmatically BLAST a sequence to a local database of all WGS assemblies.Since this isn't feasible...

Asked on 12/12/2020 by Oren Milman

1 answer

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