One of the issues of services like Innocentive is that by design they provide suboptimal solutions to seekers. Why? There’s no tweaking allowed. It is almost imp0ssible to have the situation where the winning solution is also optimal. Optimization could… Read more ›
It took me couple of days of searching the web and trying to build my own annotation database for non-model organism, before I’ve realized that Bioconductor already has a mechanism that automates the whole process. In this particular example, I… Read more ›
Here’s a set of commands to generate consensus sequence from mapping reads onto reference. This is implementation of the answer to my question “Software for gene recontruction from WGS data” on BioStar.
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bwa index database.fasta bwa aln -t $num_threads database.fasta reads.fastq > reads.sai bwa samse database.fasta reads.sai reads.fastq > aln.sam samtools view -b -o aln.bam aln.sam samtools sort aln.bam aln.sorted samtools index aln.sorted.bam samtools mpileup -uf database.fasta aln.sorted.bam |bcftools view -cg - |vcfutils.pl vcf2fq >aln.fastq |
The above code is also available as… Read more ›
There are three interesting WordPress plugins for the embedding citations into blog posts. The first, Kcite is the work by Simon Cockell and Philip Lord. Allows to cite virtually everything. There’s no “but” other than the workflow isn’t that great (have… Read more ›
Input streams: Twitter accessed through Flipboard and desktop clients (all favorited tweets are bookmarked at Diigo) Feedly (~150 subscriptions, dynamically changed) and its “saved for later” option random browsing ends up at Diigo research stuff gets downloaded into Zotero and ends up in one of the predefined… Read more ›
Very interesting research on the diversification of proteome in fungi. Alternative splicing is commonly used by the Metazoa to generate more than one protein from a gene. However, such diversification of the proteome by alternative splicing is much rarer in… Read more ›
There’s an article on Think Progress on the profits of corporations from publicly funded research. Obviously, Elsevier’s earnings had to be mentioned. Note to self: find a summary of overall profits for all major STM publishers, including OA ones. How… Read more ›
Miniproject to be done: a script to show a biodiversity of metagenomic sample on a taxonomic tree. There are quite a few options to visualize phylogenetic trees in a programmatic way. See summary by Kat Holt. Out of three (four)… Read more ›
There are many papers describing bias of amplification of 16S gene and resulting bias in assessment of biodiversity. However some interesting recent publications expand the story. There’s a nice research on including number of 16S gene copies per genome into… Read more ›