bioruby-ngs
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rjpbonnal
This plugins is intended to wrap the common software used for Next Generation Sequencing data
Task in biongs which make the mapping using tophat, has the parameter fastq. The procedure can not handle smoothly if the user has fastq.gz file but must importantly generic names...
Considering removing FastX and using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic) to perform reads trimming based on quality values. Trimmomatic is written in Java, it's multithreaded and keeps the correct pairing during the trimming,...
If the user reinstalls the gem binaries installed in common are wiped out. Provide an option to avoid this behavior '--do-not-reinstall'
With Cuffcompare it is possible to determine a unique set of isoforms for each transcripts locus integrating different annotation resources. The problem is that Cuffcompare assigns new gene_id and transcripts_id...
It seems that ActiveRecord 3.2.5 has introduced (again) major changes. Simple methods like Model.find(:all) that always worked perfectly with 3.0 now raise errors. Considering the instability AR has showed in...
Support the first step of demultiplexing without appealing to CASAVA
the REQUIREMENTS section (including dependency on gnuplot) should be moved to the top of README
Probably, file/dir name conventions should only be applied to biongs project types. To clarify, 'biongs tasks' and 'types of projects' should be described differently. Tasks are the minimum unit of...
I succeeded to run "biongs quality:fastq_stats" and "biongs quality:boxplot" but it seems that these doesn't depend on the "biongs project:new" directory structure. This is useful.
If we don't rely on the gnuplot in the near future, it would be also nice (already in TODO).