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This edition of the Herald was brought to you by contribution from zx8754, Istvan Albert, lethalfang, and was edited by Istvan Albert,
Nanopore sequencing technology, bioinformatics and applications | Nature Biotechnology (www.nature.com)
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes.
submitted by: Istvan Albert
Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study | Scientific Data (doi.org)
This is a data descriptor paper describing the multi-center and cross-platform WGS and WES data for a pair of tumor-normal cancer cell lines. The DNA was produced in a single batch to ensure sample homogeneity.
- All the data are on SRA
- Some data are also on NCBI, e.g., bwa mem aligned BAM files, etc.
- The high-confidence somatic mutation call set
submitted by: lethalfang
The overlap in DEGs between methods was surprisingly terrible. Less than 10% of the DEGs were shared by both scRNAseq and bulk RNAseq with 1ng RNA input. Most unexpected were the 20% of DEGs that were called by scRNAseq but not bulk RNAseq. What's up with that? 4/11 pic.twitter.com/qXhJIwB2AZ
— Dr. Liz Kirby, PhD (@THEKirbyLab) November 9, 2021
The overlap in DEGs between methods was surprisingly terrible. Less than 10% of the DEGs were shared by both scRNAseq and bulk RNAseq with 1ng RNA input. Most unexpected were the 20% of DEGs that were called by scRNAseq but not bulk RNAseq. What's up with that? 4/11 pic.twitter.com/qXhJIwB2AZ
— Dr. Liz Kirby, PhD (@THEKirbyLab) November 9, 2021submitted by: Istvan Albert
To single cell seq or not to single cell seq?
Ever wonder how scRNAseq data compares to bulk RNAseq? Well, we looked it using adult neural stem cells (NSCs) in our new preprint. 🧵1/11https://t.co/enYySO8mNQ
— Dr. Liz Kirby, PhD (@THEKirbyLab) November 9, 2021
To single cell seq or not to single cell seq?
Ever wonder how scRNAseq data compares to bulk RNAseq? Well, we looked it using adult neural stem cells (NSCs) in our new preprint. 🧵1/11https://t.co/enYySO8mNQ
submitted by: Istvan Albert
Author Checklist - data analysis - Datamethods Discussion Forum (discourse.datamethods.org)
Statistical Problems to Document and to Avoid - Frank Harell
submitted by: zx8754
Codetta Program Deciphers Genetic Code in 250,000 Genomes | HHMI (www.hhmi.org)
Codetta, a new computational method for predicting genetic codes, could reveal insights into how some organisms have modified a code once thought to be universal.
submitted by: Istvan Albert
GitHub - cbg-ethz/V-pipe: V-pipe is a pipeline designed for analysing NGS data of short viral genomes (github.com)
V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format (e.g., consensus sequences, SNV calls, local/global haplotypes). V-pipe is written using the Snakemake workflow management system.
submitted by: Istvan Albert
GitHub - rrwick/Trycycler: A tool for generating consensus long-read assemblies for bacterial genomes (github.com)
Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.
submitted by: Istvan Albert
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