The goal of today's practical session is to get your hands dirty with bedtools. We will be studying ChiP-seq data from three different cell types. Each cell type was assayed for H3K27ac. Our research goal is to understand and explore the similarities and differences between the ChIP peaks observed in the 3 different cell types.
Aaron Quinlan arq5x
arq5x
/ bioch5080.md
Last active
December 15, 2015 07:09
arq5x
/ gist:4686637
Created
January 31, 2013 21:28
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| { | |
| "pile": { | |
| "chrom": "chr1" | |
| "start": 102033445 | |
| "end": 102033446 | |
| "ref": "G" | |
| "total_ref_alleles": 45 | |
| "total_alt_alleles": 15 | |
| "total_fwd_a": 7 | |
| "total_rev_a": 8 |
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| HISTCONTROL="erasedups" | |
| export HISTCONTROL |
arq5x
/ kmher-install.sh
Last active
December 11, 2015 03:59
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| $ make clean | |
| cd lib && make clean | |
| rm -f *.o zlib-1.2.3/*.o zlib-1.2.3/libz.1.2.3.dylib | |
| cd python && rm -fr build khmer/*.so | |
| $ make all | |
| cd lib && make | |
| cd zlib-1.2.3; ./configure --shared; make; rm minigzip.o; rm example.o | |
| Checking for gcc... | |
| Checking for shared library support... |
arq5x
/ make-unified-segmentation.sh
Created
September 14, 2012 00:55
ENCODE consensus segmentations
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| # 1. Get the ENCODE segmentations from EBI. | |
| # consensus | |
| wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/gm12878.combined.bb | |
| wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/h1hesc.combined.bb | |
| wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/helas3.combined.bb | |
| wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/hepg2.combined.bb | |
| wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/huvec.combined.bb | |
| wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/k562.combined.bb | |
| # Segway (ahem; https://twitter.com/michaelhoffman/status/246679147164880897) |
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| # alias the raw data files | |
| ln -s C0PYJACXX_s7_0_GSL48index_10_SL16067.fastq.gz 0h-IP-nbn.fq.gz | |
| ln -s C0PYJACXX_s7_0_GSL48index_11_SL16068.fastq.gz 3Gy-IP-nbn.fq.gz | |
| ln -s C0PYJACXX_s7_0_GSL48index_12_SL16069.fastq.gz PpoI-IP-nbn.fq.gz | |
| ln -s C0PYJACXX_s7_0_GSL48index_7_SL16064.fastq.gz 0h-Input.fq.gz | |
| ln -s C0PYJACXX_s7_0_GSL48index_8_SL16065.fastq.gz 3Gy-Input.fq.gz | |
| ln -s C0PYJACXX_s7_0_GSL48index_9_SL16066.fastq.gz PpoI-Input.fq.gz | |
| # build a list of sample stubs | |
| SAMPLES="0h-Input 0h-IP-nbn 3Gy-Input 3Gy-IP-nbn PpoI-Input PpoI-IP-nbn" |
arq5x
/ config.log
Created
August 17, 2012 15:44
Homebrew error log for graph-tool installation error.
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| This file contains any messages produced by compilers while | |
| running configure, to aid debugging if configure makes a mistake. | |
| It was created by graph-tool configure 2.2.14, which was | |
| generated by GNU Autoconf 2.68. Invocation command line was | |
| $ ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/graph-tool/2.2.14 | |
| ## --------- ## | |
| ## Platform. ## |
arq5x
/ make-master-hmm.sh
Created
July 18, 2012 20:19
For Gemini: Create a master ChromHMM track from the 9 distinct cell types.
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| echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz | |
| http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \ | |
| > chromhmm-files.txt |
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| 1. Download and install the CUDA toolkit. | |
| - http://developer.nvidia.com/cuda-downloads | |
| - For Mac, http://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_macos.pkg | |
| 2. Download and install the CUDA drivers for you system. | |
| - http://developer.nvidia.com/cuda-downloads | |
| - For Mac, http://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2.10_macos.dmg | |
| 3. Download and install the cudapp library | |
| http://code.google.com/p/cudpp/ |
arq5x
/ sim-gemini-bin-genotypes.py
Created
June 20, 2012 16:19
prototype for storing/reading gemini genotypes in PLINK BED-like format
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| #!/usr/bin/python | |
| import array | |
| import gzip | |
| import struct | |
| import numpy as np | |
| import multiprocessing as mp | |
| class BinaryGenoWriter(object): |