Bioinformatics Stack Exchange Community Digest

Top new questions this week:

RNA folding at specific temperature with ViennaRNA in python

I am trying to get dot-bracket-notations of single stranded RNA via the ViennaRNA python package (pypi.org/project/ViennaRNA/) at different temperatures. I have read in the docs (www….

python rna secondary-structure

asked by gojih Score of 3

How to remove double '/' from file path, bash script

I’m using the following script to detect strandedness of my paired end RNA-seq data. …

rna-seq bash

asked by pubsurfted Score of 2 answered by Steve Score of 2

File I/O error using nglview.show_biopython(structure)

So I have been trying to get into visualizing proteins in python, so after some research I ended up on a tutorial that was teaching you how to visualize a protein from the COVID-19 virus, so I went …

python structural-biology

asked by Jeremiah Wade Score of 2

CNVKit does not output all the accessible regions in the targets bed file

This question was also asked on Biostars I am using CNVkit on my data using hg38 as reference. The command that I am using is the following: …

reference-genome bed wgs cnv

asked by ashenflower Score of 2

Input for –score in PLINK 1.9 when generationg PRS using GWAS summary statistics

I’m conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics. It is known that the GWAS will give BETA and OR for …

gwas plink polygenic-risk-score

asked by Dovini Jayasinghe Score of 2

Can I run dotPlotly from Rstudio?

I’d like to run dotPlotly from RStudio but I can’t find any description/help for this. Is it at all possible? Another side to this question: does anyone know any tool for dot plots for genome …

r ggplot2

asked by SKay Score of 2 answered by Maximilian Press Score of 1

How to extract date of acquisiton from mzXML and mzML files with Python?

I would like to extract date of acquisiton from mzXML and mzML files, using Python. Is it possible e.g. with Pyteomics? pymzml is only for mzML files. Are there other libraries that can do that? I …

python pymzml pyteomics

asked by Soren Score of 1 answered by Lev Levitsky Score of 1

Greatest hits from previous weeks:

changing color key range to specified range in heatmap.2 function

I have a tab separated text file as shown below …

r bioconductor

asked by user3138373 Score of 4 answered by Devon Ryan Score of 4

removing nextera transposase adapters, cutadapt

I am learning about NGS analysis and im currently learning about QCing and removing adaptors. I am working on SRR1972920_1.fastq file. When running fastqc tool on that file, adapter contamination …

adapter cutadapt

asked by Skepto18 Score of 3 answered by StupidWolf Score of 5

How to convert fasta file to tab delimited file

I have a fasta file like >sample 1 gene 1 atgc >sample 1 gene 2 atgc >sample 2 gene 1 atgc I want to get the following output, with one break between …

fasta format-conversion

asked by AudileF Score of 14 answered by terdon Score of 12

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. …

fasta ncbi linux

asked by MudithMMBc Score of 10 answered by dc37 Score of 10

Resolution parameter in Seurat's FindClusters function for larger cell numbers

In Seurats‘ documentation for FindClusters() function it is written that for around 3000 …

r single-cell seurat

asked by Nikita Vlasenko Score of 5 answered by Peter Score of 6

What is a quick way to find the reverse complement in bash

I have a DNA sequence for which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?

sequence-analysis dna bash

asked by winni2k Score of 11 answered by winni2k Score of 25

how to merge more than two sample in Seurat?

I would like to merge more than two sample in the Seurat, and the mergeseurat can only merge two sample. So what should I do now. The screenshot is my script.

single-cell

asked by hua Score of 2 answered by haci Score of 3

Can you answer these questions?

Feeding the output of one task into another in WDL

Hi there I’m new to WDL and I need to complete a two-step workflow, Basically, what I need to do is to extract and merge two reads dataset (forward and reverse) for a sample and pass the merged, …

wdl docker

asked by Matteo Score of 1

Visualise multiple disappearing pdb files in Pymol

I have a sequence of pdb files which I want to load in pymol window so that it gives an impression of a video. I am using cmd.load function in a loop and deleting the loaded file in the next step. But …

python pymol

asked by vipul-chem Score of 1

Reading a Fast5-file with Python

I am trying to extract data from fast5-file with python 3.9.13 in Ubuntu. I have found a library “fast5_research”(This package comprises an API to HDF containers used by the research groups …

python nanopore jupyter base-calling fast5

asked by Shwarz Score of 1 answered by M__ Score of 0