readme upd

Author: mikessh

README.md

@@ -2,20 +2,30 @@
 
 ## MiGEC: Molecular Identifier Guided Error Correction pipeline  
 
-This pipeline provides several useful tools for analysis of immune repertoire sequencing data. Its main feature is the ability to use information from unique nucleotide tags (UMIs, see this [paper](http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1778.html) for details), which are attached to molecules before sequencing library preparation and allow to backtrack the original sequence of molecule. UMIs make it possible to computationally filter nearly all experimental errors from resulting immune receptor sequences. 
+This pipeline provides several useful tools for analysis of immune repertoire sequencing data. Its main feature is the ability to use information from unique nucleotide tags (UMIs, see this [paper](http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1778.html) for details), which are attached to molecules before sequencing library preparation and allow to backtrack the original sequence of molecule. UMIs make it possible to computationally filter nearly all experimental errors from resulting immune receptor sequences.
 
 This pipeline was designed for libraries sequenced using Illumina MiSeq and HiSeq and the main requirement for sequencing reads is that they should contain the entire CDR3 region of immune receptor gene. Sequencing libraries with high over-sequencing, i.e. ones that have 5+ reads per starting molecule (unique UMI tag), should be used for optimal error elimination.
 
 Several modules of the pipeline, such as de-multiplexing and CDR3 extraction could be utilized for a wider range of datasets.
 
-Compiled binaries are available from [here](https://github.com/mikessh/migec/releases/latest).
-The software is cross-platform and requires Java v1.8 to run.
+Compiled binaries are available from [here](https://github.com/mikessh/migec/releases/latest). You can download them and execute as
+
+```bash
+java -jar migec.jar ...
+```
+
+Make sure that you've specified the full/correct path to jar file. In case of Java Heap Space exception, you can increase the JVM memory limit by adding ``-Xmx20G`` (for extra 20G) after the ``-jar`` argument.
+
+The software is cross-platform and requires Java v1.7+ to run.
+
 Easy installation on MacOS/Linux via [Homebrew](http://brew.sh/) or [Linuxbrew](http://linuxbrew.sh/):
 ```bash
+brew tap homebrew/science
 brew tap mikessh/repseq
 brew install migec
 migec Checkout ...
 ```
+See [homebrew-repseq](https://github.com/mikessh/homebrew-repseq) for other RepSeq analysis software Homebrew installers.
 
 For more details please see the [paper](http://www.nature.com/nmeth/journal/v11/n6/abs/nmeth.2960.html) describing MiGEC.
 
@@ -43,4 +53,4 @@ Have a glance at the analyzed data (done with legacy MIGEC version):
 
 * The spreadsheet demonstrating efficient error elimination for spike-in clonotypes with known sequences [[Download](https://github.com/mikessh/migec/blob/master/misc/Exp2-spikein-table.xlsx?raw=true)]
 * The spreadsheet with whole repertoire [[Download](https://github.com/mikessh/migec/blob/master/misc/Exp2-all-cdr-migec.xlsx?raw=true)]
-* An interactive network of B-cell clonal trees (created using [Cytoscape](http://cytoscape.org/)) [[Download](https://github.com/mikessh/migec/blob/master/misc/Exp2-all-cdr-migec.cys?raw=true)]
+* An interactive network of B-cell clonal trees (created using [Cytoscape](http://cytoscape.org/)) [[Download](https://github.com/mikessh/migec/blob/master/misc/Exp2-all-cdr-migec.cys?raw=true)]