Nanopore · Plotting · Python

Insertion-deletion ratio in Oxford Nanopore PromethION data

It’s been a while since I wrote another blog post, so here is something short. Today I had to figure out the inversion deletion ratio in Oxford Nanopore Sequencing data from PromethION human whole genome sequencing. I want to compare this ratio for reads which are qualified by albacore as “pass” (average base call quality score… Continue reading Insertion-deletion ratio in Oxford Nanopore PromethION data

Nanopore · Plotting

NanoPlot example gallery update

Months ago I wrote a blog post with an example gallery of plots from NanoPlot so it might be time for an update with NanoPlot v1.9.2 (currently published as a preprint together with my other long read plotting and processing scripts). The data below is from the publicly available NA12878 dataset, release5, base called by the… Continue reading NanoPlot example gallery update

Plotting · R · transcriptomics

Identifying an individual with Klinefelter syndrome in transcriptome sequencing

In my previous post, I showed how to infer the sex of individuals from transcriptome sequencing. I applied this to a different dataset, and the result (shown below) has a remarkable outlier: sample 34. The title is already a big spoiler: it turns out that this individual has Klinefelter syndrome (47,XXY), a male with two X… Continue reading Identifying an individual with Klinefelter syndrome in transcriptome sequencing

Plotting · R

Inferring the sex based on transcriptome sequencing

Analogous to my previous post on inferring the sex of individuals based on exome sequencing I’ll now show you how to do the same for transcriptome sequencing. In the example, I use data from Lexogen QuantSeq but this is most likely equally applicable to other RNA-seq approaches. This is a useful QC step and can detect… Continue reading Inferring the sex based on transcriptome sequencing

Coding · Plotting · Python

Inferring the sex based on exome sequencing

So today I came across the annoying issue that someone had not bothered to document the sex of samples, even when we generated exome sequencing data of those. So I wrote a script to figure this out based on coverage on the X and Y chromosomes, but not in the pseudoautosomal regions. The script can… Continue reading Inferring the sex based on exome sequencing

Coding · Plotting · Python

Altmetric scores for bioRxiv preprints, part 2

This post is part of the series starring altmetric attention scores and bioRxiv preprints, see also the earlier post about my Twitter bot, getting the altmetric scores and part 1 of the analysis. Today I’ll have a look at the top 10% altmetric scores and how fast the preprint got that score. These are the articles… Continue reading Altmetric scores for bioRxiv preprints, part 2

Plotting · Python

Altmetric scores for bioRxiv preprints, part 1

This post is following my earlier posts about my Twitter bot for interesting preprints and how to get altmetric scores for all bioRxiv preprints. In this post, I want to take a first look at the obtained data. I’ll do this using the Python pandas module. When working with pandas DataFrames interactively it’s convenient to… Continue reading Altmetric scores for bioRxiv preprints, part 1