From f57543851be30d57fc27556b390c034a00b98792 Mon Sep 17 00:00:00 2001
From: Manuel Irimia <mirimia@gmail.com>
Date: Mon, 6 May 2019 00:24:03 +0200
Subject: [PATCH] Update in README to include min_ALT_use info

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 38b6ddb..a6528c2 100644
--- a/README.md
+++ b/README.md
@@ -353,6 +353,8 @@ will identify those AS events with an absolute ΔPSI between A and B higher than
 
 By default, the comparison is not paired. A paired analysis can be done using the option ``--paired``. If provided, each A replicate is compared with the corresponding one in group B. In this case, ``--min_dPSI`` is the minimum threshold for the average between each pair's ΔPSI, and ``--min_range`` is the minimum value *any* individual pair's ΔPSI can be (i.e. all individual ΔPSI's absolute values have to be larger than the value provided as ``--min_range`` and they all have to have the same sign [positive or negative]). 
 
+From v2.2.1, `compare` also requires that Alt3 (ALTA) and Alt5 (ALTD) events with differential splice site usage have a predicted significant overall impact in the transcript pool. Therefore, `compare` requires that the alternative splice sites being compared belong to an exon with a minimum inclusion level (~PSI) across ALL compared samples. This minimum PSI for the host exon is set to 25 by default, and can be modified using the `--min_ALT_use` option. The equivalent value to previous versions is `--min_ALT_use  0`.
+
 Summary statistics are printed for a tally of AS events by type that show higher sequence inclusion in group A or B, the total number of events in ``vast-tools`` that have been profiled (i.e. that pass any applied filter), and the subset of the latter that are alternatively spliced in at least one of the compared samples (10<PSI<90).
 
 Differentially spliced AS events are printed out to an output file. The name of this file is generated by default based on the parameters used, but it can also be provided using ``--outFile``. The file is created in the directory of the input file. The selected events are then plotted automatically using ``vast-tools plot`` (see below), using a config file generated based on the type and order of the replicates provided as input. By default, all samples in the INCLUSION file are plotted, but it is possible to plot only the compared samples providing the ``--only_samples`` option. The plotting step can be skipped by activating the ``--no_plot`` flag.