Improved documentation: Step 1. Prepare the LeafCutter differential splicing results for visualisation about leafcutter HOT 3 CLOSED

Completely agree, and this interface needs cleaning up.

For the example YRI vs EU data it should be something like this:

../leafviz/prepare_results.R -i . -o for_leafviz --support test_diff_intron.txt --annotation_code ../leafviz/annotation_codes/gencode_hg19/gencode_hg19 --code leafcutter

but you'd need to move testYRIvsEU_perind_numers.counts.gz to leafcutter_perind_numers.counts.gz which we shouldn't require.

from leafcutter.

This is done. The interface to prepare_results.R is simplified, the dependence on bedtools has been removed and the documentation shows how to run the example from Usage.

from leafcutter.

@davidaknowles
May I ask if I need to get the FDR value of each intron instead of cluster, does leafcutter provide the corresponding code?

from leafcutter.