Cheap Z-stage (SELN LZ-60 Shengling Precise Machinery CO. Ltd)

I picked up this cheap Chinese Z-stage on ebay, it was only 100USD and I wasn’t expecting much but it’s actually pretty well put together. It uses a standard micrometer head and I could fit both a Picomotor and the Chuo Seiki AMH-13 in its place (which works well). The micrometer head provided (pictured below) …

Chuo Seiki AMH-13

I picked up a X stage which uses a Chuo Seiki AMH-13 auto micro. The auto micro uses a coreless DC motor and of course came without a driver. It turned out to be pretty simple to drive, requiring only a DC voltage somewhere in the region of 1 and 5V. When I was testing …

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 …