The major new feature in SeqMonk v0.30.x was the introduction of a bridge between SeqMonk and R, which allows the program to transparently run analyses in R from within the SeqMonk interface. This functionality makes it very easy to run popular algorithms such as DESeq and EdgeR without having to write custom scripts or go…
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Why is java not found on the command line after I’ve installed it?
The Problem A common problem we have reported from users of SeqMonk is that when they try to launch the program on a Windows system they get an error message saying that java could not be found, even though they have installed this and they can show that it works fine in their browser. When…
Importing RNA-Seq data into SeqMonk
Introduction Mapped RNA-Seq data coming from eukaryotes is probably the most complicated data type to import into SeqMonk due to it’s relative complexity and the abundance of options with which you are presented. Depending on exactly what sort of information you want to know about your data different data import options will be useful, so…
Adding custom chromosome name mappings into SeqMonk
When loading data into SeqMonk the program has to try to connect the chromosome names used in your data file with those which are present in the genome one which your project is based. In many cases there won’t be an exact match between the two – many mapping programs report file names in their…