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Update README.md #4

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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -21,7 +21,7 @@ source("http://bioconductor.org/biocLite.R")
biocLite("IRanges","BSgenome.Hsapiens.UCSC.hg19")
```

####Usage:
#### Usage:
```
./hotspot_algo.R
--input-maf=[REQUIRED: mutation file]
Expand All @@ -42,7 +42,7 @@ Command to run hotspot algorithm on genes listed in file genes_of_interest.txt:
--output-file=sig_hotspots.txt
```

####Contents:
#### Contents:
**[ Required ]** `hotspot_algo.R` - R script to execute hotspot detection algorithm

**[ Required ]** `hotspot_algo.Rdata` - Rdata object with necessary files for algorithm (mutability, expression filters, etc)
Expand All @@ -53,7 +53,7 @@ Command to run hotspot algorithm on genes listed in file genes_of_interest.txt:

`minimalist_test_maf.txt` - minimalist MAF needed from maf2maf. [mskcc/maf2maf](https://github.com/mskcc/vcf2maf)

####Notes:
#### Notes:
`--align100mer` and `--align24mer` are optional filters based on how uniquely k-mer sequences align to a region of the hg19 genome. Note, both filters were used as part of this analysis. See more information at [ENCODE Mapability](http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability).

The use of these filters will require downloading the 100-mer and 24-mer alignability tracks from UCSC that are not included here:
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