June 7, 2015, 10:38 pm
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) is easily the nicest micrometer I’ve seen come out of China. Very smooth and clean, there does seem to be a small amount of grit left in there but overall very nice (particularly considering the price).
The linear guides also look very nice, and the overall operation of the stage is very smooth.
June 3, 2015, 9:24 pm
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.
May 28, 2015, 5:51 am
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
May 28, 2015, 5:34 am
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
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