Coding · google docs · Python

Getting the number of characters of Google documents

I did something very similar to my previous post of a couple of days ago, in which I take the sum of the number of characters of each document in a google drive folder. Today I adapted the code slightly to query individual documents, and added a Class for Documents with a method for counting… Continue reading Getting the number of characters of Google documents

Coding · google docs · Python

Getting number of characters from all documents in Google drive folder

I should be writing on my PhD thesis, but instead I wrote a fun piece of code. I wanted to trace the number of characters in my thesis documents, which are in a folder in my Google drive.  Google drive has a useful API, but with seemingly outdated and/or hard to navigate documentation (and not the… Continue reading Getting number of characters from all documents in Google drive folder

Nanopore

PromethION human genome NA19240

TLDR: we sequenced a human genome, NA19240, to 80x coverage using the Oxford Nanopore PromethION. The data is freely available on ENA. We have been sequencing on Oxford Nanopore PromethION since February. Our main interest is in structural variation in the context of neurodegenerative diseases such as Alzheimer Disease and Frontotemporal Dementia, but for benchmarking… Continue reading PromethION human genome NA19240

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