bedtools merge book-end merge
I never paid too much attention to this (I should have), but TIL that bedtools merge default is not only to merge overlapping regions but also to merge book-ended regions. From the bedtools merge manual: -d Maximum distance between features allowed for features to be merged. Default is 0. That is, overlapping and/or book-ended features…
Extract a single sample from multi-sample VCF
Sometimes you want to subset/extract just a single sample from a large multi-sample VCF. In my case, we wanted to get per-sample VCF from the 1000 Genome Project. As there is always more than one way to skin a cat, I compared vcftools and bcfools. It turned out bcftools is ~50% faster than vcftools and…
Is stop codon part of CDS? Yes, but GTF format is “special”
Recently, I was going through a mix of gene annotation GTFs from different sources and had to fix them. One of the differences was the annotation of stop codons. More specifically, whether the stop codon was part of the annotated CDS (coding sequence). I had to refresh my biology knowledge and biologically speaking, stop codon…
htmlwidgets::saveWidget Error: pandoc document conversion failed with error 97
I always use htmlwidgets::saveWidget to save my Plotly html plots in R. For some unknown reason, I started to get: I first thought I had some problems with the temp dir so I tried to add dir.create(tempdir()) but it wasn’t it. After some more digging I found this GitHub issue and answer from cpsievert, which…
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Jan's Blog of Bioinformatics Bits 