Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 6

Is there a computational method/method/way to predict if a cell population in a tissue immigrated or is enriched locally?

I have single cell data which I have analysed for differential expression. In my experiment, I subjected two groups of mice (a control and a treatment group) to treatment...

Asked on 09/27/2021

1 answer

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

I want to add the frequencies of the genotypes to a baseline of raw DNA data I've got from the DNA testing companies 23andMe, Ancestry and MyHeritage (tested at all)....

Asked on 09/26/2021 by a4xrbj1

2 answer

Obtaining HGDP project data in fasta format

I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the...

Asked on 09/26/2021

1 answer

Download or create VCF from Human Genome Diversity Project (HGDP)

I can't seem to find HGDP data in VCF format. Does anyone know where I can download it from? Perhaps there a Snakemake pipeline for calling VCFs from this data?...

Asked on 09/26/2021

1 answer

How to generate Beta diversity boxplot from phyloseq object?

I am working with profiled metagenomic taxonomy abundance data. I want to generate beta diversity (bray-curtis) boxplot from a phyloseq object where two groups (control and test) will be shown....

Asked on 09/25/2021

1 answer

Weird phylogenetic tree

I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding...

Asked on 09/25/2021 by Zaci

1 answer

How to define an outgroup to build a robust amino acid tree

I building a robust amino acid phylogeny with adequate robustness support (see previous post here). This is a brief summary of what I have done:I performed a BLASTp analysis...

Asked on 09/25/2021 by Leah

2 answer

Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?

This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback...

Asked on 09/05/2021

1 answer

Split fasta file based on groups in header information and output as separate files

I have a fasta file containing the sequence of a gene across different species. In total there are around 900 samples and 12 species. (Each sequences is over multiple lines...

Asked on 09/04/2021

1 answer

Difference between genome assembly and genome sequence alignment to a reference to find structural variants

I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations.I've been scouring...

Asked on 09/04/2021 by M4r1n4

1 answer

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