Basic bowtie2 alignment notes

It’s equally been a while since I’ve driven bowtie, and now there’s bowtie2. Basic alignment notes: And out pops a SAM file. This can be converted to a BAM with samtools: For blog updates and more follow me on twitter.

Using BLAST+ for nucleotide alignments

It’s quite some time since I needed to run BLAST locally on anything. Here are some quick notes. First download BLAST: Create a new reference database: In my case I needed to align fastq files. However BLAST only takes fasta. I used to the following to convert the fastqs to fastas: And finally run the …

Interfacing Chuo Seiki stages

I finally got a chance to setup the Chuo Seiki motorized stages I bought at auction a while back. The stages use oriental motor 5 phase stepper motors (PH533s). Of course, being second hand they didn’t come with any drivers, and stepper 5-phase drivers are far less common than 2-phase ones. I picked up an …

Axopatch 200A Internal Pics

I picked up an Axon instruments Axopatch 200A on ebay (it’s a patch clamp which can be used for ion channel experiments among other things). Here are some PCB pics for your viewing pleasure. No headstage pictures yet, but I’ll add them at some point. Late 80s early 90s electronics at its finest! For blog …