Even `bowtie2`’s `–very-sensitive-local` option can be a little grumpy. Here’s how I make `bowtie2` a little more relaxed for alignment of more dissimilar sequences, particularly for my work on metagenomes.
I am not a very organised bioinformatician, and despite your best efforts, you probably aren’t either. I’ve written a tool called `chitin` that tries to keep me, and bioinformatics more organised.
I’m published! I’m a real scientist now! Check out the application note on Bioinformatics.
I wanted a BAM that contained reads aligned to just one of the many contigs the file contained. As usual, I made this much more difficult than it really ought to have been.
This afternoon I wanted to quickly check whether some reads in a BAM would be filtered out by the GATK `MalformedReadFilter`. Turns out that GATK is pretty unforgiving if you forget that filter is automatically applied by `PrintReads`.
Recently I’ve been following the GATK DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.
As a curious and nosy individual who likes to know everything, I wrote a script dubbed memblame which is responsible for naming and shaming authors of “inefficient”1 jobs at our cluster here in IBERS. It takes time, often days, sometimes longer, of patience to see large-input jobs executed on a node on the compute cluster […]