From 170e06c558d5f627a7ee13931864f371cca51ffc Mon Sep 17 00:00:00 2001 From: "David A. Knowles" Date: Tue, 19 Sep 2017 16:03:11 -0700 Subject: [PATCH] Updated docs --- docs/articles/Usage.html | 4 +++- docs/articles/Visualization.html | 14 +++++++------- docs/articles/index.html | 2 +- docs/reference/dirichlet_multinomial_anova_mc.html | 6 +++--- docs/reference/index.html | 2 +- leafcutter/DESCRIPTION | 4 ++-- leafcutter/vignettes/Usage.Rmd | 7 ++++++- 7 files changed, 23 insertions(+), 16 deletions(-) diff --git a/docs/articles/Usage.html b/docs/articles/Usage.html index 488d410..916baa3 100644 --- a/docs/articles/Usage.html +++ b/docs/articles/Usage.html @@ -98,8 +98,10 @@

where -j provides a custom junction file, and -e specifies the required number of nt the read must extend into the exon to be quantified. For more details on the junction file we used see Li et al. 2005.

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 ) and alignment itself was run as

+

(alternatively use one of the prebuilt indices ) 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

diff --git a/docs/articles/Visualization.html b/docs/articles/Visualization.html index 97b4c3c..120b2c6 100644 --- a/docs/articles/Visualization.html +++ b/docs/articles/Visualization.html @@ -76,20 +76,20 @@

Leafcutter Shiny App

Example

-

If you’ve already installed leafcutter then you can easily fire up a local shiny app on the same GTEx example data. Navigate into the leafviz directory:

-
cd leafviz
+

If you’ve already installed leafcutter then you can easily fire up a local shiny app on the same GTEx example data. Navigate into the leafvis directory:

+
cd leafvis

and then download the example data using

./download_example.sh

This will download and unzip a folder called example. Now starting the shiny app should be as easy as

-
./run_leafviz.R example/Brain_vs_Heart_results.Rdata
-

You can even leave out the example/Brain_vs_Heart_results.Rdata part as this is the default dataset run_leafviz.R will try to use.

+
./run_leafvis.R example/Brain_vs_Heart_results.Rdata
+

You can even leave out the example/Brain_vs_Heart_results.Rdata part as this is the default dataset run_leafvis.R will try to use.

Annotation code

The Shiny app includes functionality to label detected introns as annotated or cryptic. To do for a new dataset this an “annotation code” is needed, built from a “Gene Transfer Format” file appropriate for your genome. We provide pre-built annotation codes for hg19 and hg38 which can be downloaded by running

./download_human_annotation_codes.sh
-

from the leafviz directory. To build a new annotation code you need:

+

from the leafvis directory. To build a new annotation code you need:

  • bedtools >= v2.17.0
    • @@ -158,8 +158,8 @@

    Step 2. Visualise the results

    -
    cd leafviz/
-Rscript run_leafviz.R <oFolder>/results/<code>_results.Rdata
    +
    cd leafvis/
+Rscript run_leafvis.R <oFolder>/results/<code>_results.Rdata

    This will load in the Rdata object and run the LeafCutter Visualisation App in your browser.

    diff --git a/docs/articles/index.html b/docs/articles/index.html index 67eaad3..770eebe 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@
    -

    Articles version 0.2.4

    +

    Articles version 0.2.6

    diff --git a/docs/reference/dirichlet_multinomial_anova_mc.html b/docs/reference/dirichlet_multinomial_anova_mc.html index 937547f..a689d18 100644 --- a/docs/reference/dirichlet_multinomial_anova_mc.html +++ b/docs/reference/dirichlet_multinomial_anova_mc.html @@ -96,7 +96,7 @@

    Dirichlet multinomial GLM likelihood ratio test for a single cluster

    dirichlet_multinomial_anova_mc(xFull, xNull, y, concShape = 1.0001,
   concRate = 1e-04, robust = T, outlier_prior_a = 1.01,
   outlier_prior_b = 100, fit_null = NULL, debug = F, init = "smart",
-  ...)
    + smart_init_regularizer = 0.001, ...)

    Arguments

    @@ -146,8 +146,8 @@

    Ar

    - - + +

    Can be one of "smart", "random". smart uses an method of moments estimator to get a reasonable initialization. The seed for "random" can be set through the ... arguments passed to rstan::optimizing.
    ...

    will be passed on the rstan::optimizing, so can be used for example to set the algorithm used (default is LBFGS) or the random seed if random initialization is requested.

    		#'

    @param ... will be passed on the rstan::optimizing, so can be used for example to set the algorithm used (default is LBFGS) or the random seed if random initialization is requested.
    diff --git a/docs/reference/index.html b/docs/reference/index.html index 796e1a8..d9a4da9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -88,7 +88,7 @@

    Reference - version 0.2.4 + version 0.2.6

    diff --git a/leafcutter/DESCRIPTION b/leafcutter/DESCRIPTION index 380cfb6..42c7d83 100644 --- 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 index 5444ad8..567d25b 100644 --- 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).