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

Nanopore · Plotting

Calculated average quality vs. Albacore summary

I discussed earlier the difference between a) the calculated per read average basecall quality and b) the quality score given by albacore in the sequencing_summary file. Today I had a closer look at this difference and for one dataset I calculated the average quality from the fastq file and compared that to the accompanying sequencing_summary. The… Continue reading Calculated average quality vs. Albacore summary

Nanopore · Plotting

Median basecall quality score to estimate accuracy

I’ve had a few posts already about basecall quality scores and how those compare to the percent identity of the reads. This post is again a short follow-up on those stories. Today I investigate whether the median basecall quality (Phred) score of the aligned fragments is a good or better estimator for the percent identity… Continue reading Median basecall quality score to estimate accuracy

Nanopore · Plotting

The distribution of basecall quality scores

I also investigated the Oxford Nanopore quality scores in some of my previous posts, and this post is a follow-up of those. Today I investigate the distribution of the basecall quality scores and how the mean and median per read behave. At the bottom of this post is the script I used to generate the… Continue reading The distribution of basecall quality scores