Unanswered Questions

749 questions with no upvoted or accepted answers
10
votes
0answers
138 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 ...
9
votes
0answers
132 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 ...
7
votes
1answer
269 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 ...
7
votes
0answers
83 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 ...
7
votes
0answers
57 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 ...
7
votes
0answers
301 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 ...
6
votes
0answers
92 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 ...
6
votes
0answers
221 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 ...
5
votes
0answers
29 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. ...
5
votes
0answers
70 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 ...
5
votes
0answers
140 views

Sequence alignment using BWT

My Problem: Skipping some specific background, what I want to do is judging whether some soft-clipping sequences are the same, which may result by the same SV event. Colored bases in Fig.1 is an ...
5
votes
0answers
65 views

Help with identifying disease modules

I've made an application that at this point ranks all combinations of drug pairs relevant to a biological network/graph in the order of how disruptive the outcome of deleting the targets of a given ...
5
votes
1answer
435 views

Voom function from limma package and Normalization on counts data

I know that Voom function from limma package from Bioconductor converts raw counts into log-CPM values and then Normalization is applied on that, with normalize.method argument. I would like to know ...
5
votes
1answer
395 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 ...
4
votes
1answer
109 views

Comparing phylogenetic models with different datasets

I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...

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