586 questions with no upvoted or accepted answers
308 views

### State of the art mutation simulation software

There are many features affecting mutation probabilities, e.g. CpG mutations are 10-fold more likely than other types of mutations. Is there a model (preferably with software) which can take two ...
94 views

### scRNA-seq multi-dataset integration for small datasets

There have been a few methods proposed for integration (or batch correction) of scRNA-seq datasets, such as Seurat CCA, MNN Correct, Scanorama, and Harmony. The concern is generally about the maximum ...
118 views

### Chimera Alignments

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want ...
80 views

### Run cuffcompare in strand-agnostic mode

Is there a way to run Cufflinks' cuffcompare in a strand-agnostic mode? I would like to do this because I have some RNA-seq datasets derived from an unstranded run, that should be compared to a ...
49 views

### Minimizing Grid Mapping time of Protein Surface

This is an interesting problem - I was wondering if anyone has a creative solution. So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
295 views

### Improving consensus assembly from UMI-tagged nanopore reads

The Albertsen lab has recently put out a competition/challenge for read error correction I only found out about this today, and I think the conference where high-ranking participants were going to be ...
233 views

### wtdbg2: practical implications of k-mer fsize and psize choice

I am using wtdbg2 2.3 to assemble a human genome (sequenced on PromethION from a cell line). I filtered out reads with low average quality, and now I am trying to determine the parameters that will ...
66 views

### Why are TPMs per 10k or 100k in many scRNA-seq studies?

I noticed that many scRNA-seq papers normalize TPMs to 10k or 100k as opposed to 1M (as the abbreviation defines them). It doesn't really matter since you are just moving the decimal point, so why ...
191 views

### How can I read multiple different regions from a BAM file?

I’m trying to process BAM records (of a coordinate-sorted, indexed BAM file) successively in fixed-size, non-overlapping, sliding genome coordinate windows. Unfortunately I am unable to read records ...
26 views

### Help with 1D^2 library shearing

I've done my 1st trial of 1D^2 whole genome sequencing using LSK-SQK308 kit with R9.5 flowcell. Without doing library fragmentation, I encountered the unexpected library shearing during sequencing. ...
55 views

### making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)?

Hi I'm a first time user of IADMIX. I tested on one known Finnish sample from the 1000Genome project using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is ...
132 views

### vcftools: indel size histogram command returns empty file

I would like to get some summary statistics on a vcf file from one individual, which has over a million variant calls. I've tried to make a histogram of indel sizes with this command, ...
390 views

### Voom function from limma package and Normalization on counts data

I know that Voom function from limma package converts raw counts into log-CPM values and then Normalization is applied on that, with normalize.method argument. But I would like to know clearly how ...
352 views

### Download data from the Human Microbiome Project via ascp

I have asked this question in biostars, but I am trying here as well as people working with "omics" data might be able to help. I think my issue relates understanding how large data storage on online ...
67 views

### which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...

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