chromHMM lab

ChromHMM/README.md

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+In this week we are taking a look at another HMM based tool, ChromHMM.
+
+  * [Project website](http://compbio.mit.edu/ChromHMM)
+  * [Manual](http://compbio.mit.edu/ChromHMM/ChromHMM_manual.pdf)
+
+### What ChromHMM does
+
+ChromHMM uses a multivariate HMM model to discover epigenomic features on a given chromosome.
+Instead of sequence data, it uses experimental results mapping epigenomic (methylation, histone modification etc.) features to the chromosome.
+
+## The difference from previous HMMs we have seen
+
+  * The alphabet size is 2 (binary) : each feature either exists or not
+  * There are multiple 'tracks' (sequences, variables ..) : these are multiple experiments done on the same chromosome
+
+### How to get ChromHMM
+
+ChromHMM is written in Java.
+Java is preferred for some projects because just like Python, users do not have to compile it, but it runs much faster compared to Python.
+*(It is however not quite as fast as native C/C++ and just almost as cumbersome to to code in.)*
+If we have java already installed, we can [download](http://compbio.mit.edu/ChromHMM/ChromHMM.zip), unzip and be ready to run ChromHMM by doing :
+
+```
+wget http://compbio.mit.edu/ChromHMM/ChromHMM.zip
+unzip ChromHMM.zip
+cd ChromHMM
+```
+
+### How to run ChromHMM
+
+As usual, the detailed specifications on how to run ChromHMM can be found in the [manual](http://compbio.mit.edu/ChromHMM/ChromHMM_manual.pdfhttp://compbio.mit.edu/ChromHMM/ChromHMM_manual.pdf).
+
+Unfortunately, we need a specific type of data to run ChromHMM (experimental mapping of epigenomic features to chromosome) but fortunately, it comes with some sample data.
+
+We can look at the sample data in the SAMPLEDATA_HG18 directory.
+One of them looks like this :
+
+```
+GM12878	chr11
+CTCF	H3K27ac	H3K27me3	H3K36me3	H3K4me1	H3K4me2	H3K4me3	H3K9ac	H4K20me1	WCE
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+0	0	0	0	0	0	0	0	0	0
+```
+
+Of course we see mostly zeroes because the beginning of the chromosome does not have many epigenomic markers, but we can see the structure.
+
+  * The first line specifies **cell name** and **chromosome name**.
+  * The second line specifies the **names of the markers**.
+  * The remaining lines specify the presence of those markers in each 200 base segment of the chromosome. 1 means present and 0 means not present.
+
+Once we have such a file, running ChromHMM is a single line operation such as :
+
+```
+java -jar ChromHMM.jar LearnModel SAMPLEDATA_HG18 test_output 4 hg18
+```
+
+Where