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updated links to HMCan and GCCount in readme #2

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updated links to HMCan and GCCount in readme #2

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d19fa8c
updated links to HMCan and GCCount in readme
favorov Nov 16, 2022
8a2e82f
added a test to run from a gui
favorov Apr 7, 2023
2a08708
Fixed the interaction btw setwd and relative file names
favorov Apr 7, 2023
abd0351
to normalizePath on mac, we need an existing file name
favorov Apr 8, 2023
83b3c31
fixed the bug when spript died if there were not enough intervals to …
favorov Apr 10, 2023
829b56d
returns to original work dir, it is useful if we run from r/rgui/rstudio
favorov Apr 10, 2023
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -17,8 +17,8 @@ Here is step-by-step instuctions how to detect super-enhancers in cancer data wi
1. Remove low quality reads (Q\<20 with `samtools view -q`) and remove duplicates from the BAM files ("samtools rmdup")
`samtools view -u -q 20 $DATAIN/XXX.bam | samtools rmdup -s - $DATAOUT/$CL.K27ac.Q20.noDup.bam`
`samtools view -u -q 20 $DATAIN/YYY.bam | samtools rmdup -s - $DATAOUT/$CL.Input.Q20.noDup.bam`
2. Call peaks with HMCan: http://www.cbrc.kaust.edu.sa/hmcan/
By default, the size of genomic regions to perform copy number normalization is 100Kb. In case you have 30M reads in the input, you can decrease this size to 10Kb if you wish. It is mostly important if you expect to have some amplifications in your tumor genomes. In this case, you will need to generate a GC content profile for such windows (use [this tool](http://www.cbrc.kaust.edu.sa/hmcan/GCCount.tar.gz)) or kindly ask Haitham Ashoor to do it for you.
2. Call peaks with HMCan: https://github.com/BoevaLab/HMCan
By default, the size of genomic regions to perform copy number normalization is 100Kb. In case you have 30M reads in the input, you can decrease this size to 10Kb if you wish. It is mostly important if you expect to have some amplifications in your tumor genomes. In this case, you will need to generate a GC content profile for such windows (use [this tool](https://github.com/BoevaLab/HMCan/tree/master/Utils/GCCount)) or kindly ask Haitham Ashoor to do it for you.
3. [Optional: bigWig files can be created automatically later by `runLILY.R`]
Create bigWig files (.bw) from HMCan density (.wig) files:
`file=$CL.K27ac.wig`
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