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davidaknowles · Sep 19, 2017 · 170e06c · 170e06c
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diff --git a/docs/articles/Usage.html b/docs/articles/Usage.html
diff --git a/docs/articles/Visualization.html b/docs/articles/Visualization.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/reference/dirichlet_multinomial_anova_mc.html b/docs/reference/dirichlet_multinomial_anova_mc.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/leafcutter/DESCRIPTION b/leafcutter/DESCRIPTION
@@ -2,8 +2,8 @@ Package: leafcutter
 Type: Package
 Title: Alternative splicing quantification, differential splicing and splicing
     QTL mapping
-Version: 0.2.5
-Date: 2017-09-07
+Version: 0.2.6
+Date: 2017-09-19
 Authors@R: c(person("David", "Knowles", email = "knowles84@gmail.com", role = c("aut", "cre")),
               person("Yang", "Li", role = c("aut", "cre")),
 			  person("Jack", "Humphrey", role = c("aut", "cre")),

diff --git a/leafcutter/vignettes/Usage.Rmd b/leafcutter/vignettes/Usage.Rmd
@@ -36,11 +36,16 @@ The `STAR` index was generated as
 ```
 STAR --runMode genomeGenerate --genomeDir hg19index/ --genomeFastaFiles hg19.fa --sjdbGTFfile gencode_v19.gtf --sjdbOverhang 100
 ```
-(alternatively use one of the [prebuilt indices](http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/) ) and alignment itself was run as
+(alternatively use one of the [prebuilt indices](http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/) ) and alignment itself was run (with STAR v2.5.2a) as
 ```
 STAR --genomeDir hg19index/ --twopassMode --outSAMstrandField intronMotif --readFilesCommand zcat --outSAMtype BAM
 ```
 
+As of STAR v2.5.3a you may need to do
+```
+STAR --genomeDir hg19index/ --twopassMode Basic --outSAMstrandField intronMotif --readFilesCommand zcat --outSAMtype BAM Unsorted
+```
+
 #### Choice of 6nt overhang
 
 We chose 6nt as the default overhang required by LeafCutter. By chance we would expect one match every 4^6^bp, or 4096bp, which appears to be quite likely for any given intron. However, RNA-seq mappers already deal with this problem by 1) assuring that the junction has already been previously annotated or is supported by reads with longer overhang (e.g. in STAR two-pass mode) 2) penalizing non-canonical junctions (i.e. non GT-AG junctions). The effect of the latter is that we would only expect one match every 4^8^bp, or 65,536bp (just one or two every 100kb, the max size allowed for our introns). However, our most restrictive filter is the requirement that reads considered be uniquely mapped. Therefore, even when the overhang is just 6bp, there is no ambiguity in mapping. Moreover, junctions are rarely only supported by reads that have an overhang of 6, when the size of the overhang goes up to 7, 8, or 9nt, the probability that we see these by chance goes down to one in over 4 million bp (for 9nt).