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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 it I set the current limit to 200mA and it appeared to consume between 100 and 200mA.
It’s equally been a while since I’ve driven bowtie, and now there’s bowtie2. Basic alignment notes:
./bowtie2-build ~/genomics/myreferece.fasta myreference
./bowtie2 -x myreference -q myreads.fastq -S ./al.sam
And out pops a SAM file. This can be converted to a BAM with samtools:
./samtools faidx ~/genomics/myreference.fasta ./samtools import ~/genomics/myreference.fasta.fai ./al.sam ./al.bam
It’s quite some time since I needed to run BLAST locally on anything. Here are some quick notes.
First download BLAST:
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.30+-x64-linux.tar.gz tar xvzf ncbi-blast-2.2.30+-x64-linux.tar.gz cd ncbi-blast-2.2.30+/bin
Create a new reference database:
./makeblastdb -in ~/genomics/myreference.fasta -dbtype nucl
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:
awk 'BEGIN{n=0;}{if(n%4 == 0) print ">" substr($0,2); if(n%4 == 1) print $0;n++;}' input.fastq > output.fasta
And finally run the alignment:
./blastn -db ~/genomics/myreference.fasta -query ./output.fasta
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 oriental motor UDK5214NW 5-phase driver. Looking at the stage it seemed that only 5 wires went to the stepper, the rest go to limit switches (I assume optical). 5 wires doesn’t seem to match with the PH533 datasheet, and the colors didn’t match those shown on the driver but I tried wiring it up anyway (I assume it uses the wiring shown below).
The most painful part of the whole process is obtaining the connectors. The stage uses HR10A-10P-12S (Hirose) connectors which cost about 20USD each. The stepper driver uses a CN1 connector which also costs about 15USD. So for an XYZ stage you’re spending 100+USD on connectors alone. It would in fact be straight forward to hack the Hirose connectors off and stick D-type connectors on but I didn’t want to mess up the stages.
Pins 1 to 5 on the HR10A appear to go to the motor. I wired these through to the stepper driver ignoring the color coding on the driver. Somewhat surprisingly this worked.
Pins 1 and 2 rotate clockwise, 3 and 4 anti-clockwise. The inputs are opto-isolated, and require a ground and signal connection.
I tried the following stages: ALV-600-H1M, ALS-602-HOM and MMU-60X-H1. They all appear to have the same pinout.
Using a 100Hz pulse it took approximately 10s to move 1mm, which sits well with the stated 1 micron resolution of these stages.
Misc. Pictures:
My name is Nava Whiteford. I’ve worked for a few sequencing companies. I have equity in a few sequencing companies based on my previous employment (I try to be unbiased in my posts). You can contact me at: [email protected]
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