Improved documentation: Step 1. Prepare the LeafCutter differential splicing results for visualisation

[AMChalkie]

This part is unclear and an example that exactly matched the results from http://davidaknowles.github.io/leafcutter/articles/Usage.html would be really helpful.

Rscript prepare_results.R --iFolder
--oFolder
--support
--annotation_code <annotation_code>
--code
--FDR \
iFolder - the folder that contains the results of the differential intron excision analysis. The script assumes all results share the same path and code.

oFolder - the folder where the results will be written.

support - the same support file as used for the previous analysis.

annotation_code - as before.

code - the same code used for the rest of the analysis, eg testYRIvsEU

FDR - the benjamini-hochberg false discovery rate with which to filter the results.

[davidaknowles]

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.

[davidaknowles]

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.

[zhengjiantao]

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