What is GCAP
GlobalChromatinAccessibilityPipelineX-nase(Dnase, Bnase, Cnase) Quality analysis pipeline
Prototype Features
See the google docs specification.[^1]
[^1]: ENCODE version
Installation
Tested version of software bundled.
| software | version | url |
|---|---|---|
| python(for pipeline) | 3.3 | https://www.python.org/ftp/python/3.3.3/Python-3.3.3.tgz |
| python(for hotspot) | 2.7 | http://www.python.org/ftp/python/2.7.6/Python-2.7.6.tgz |
| R | 3.1.1 | http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.1.tar.gz |
| bwa | 0.7.7 | https://github.com/lh3/bwa |
| fastqStatsAndSubsample | 2 | https://github.com/ENCODE-DCC/kentUtils |
| edwBamFilter | 2 | https://github.com/ENCODE-DCC/kentUtils |
| edwBamStats | 2 | https://github.com/ENCODE-DCC/kentUtils |
| samtools | 0.2.0 | https://github.com/samtools/samtools |
| bedops | 2.4.2 | https://github.com/bedops/bedops/releases/download/v2.4.2/bedops_linux_x86_64-v2.4.2.tar.bz2 |
| hotspot | 4 | https://github.com/rthurman/hotspot/archive/4.0.0.tar.gz |
| macs | 2 | macs2 2.0.10.20120913 |
| bedtools | 2.17.0 | http://github.com/arq5x/bedtools/archive/v2.17.0.tar.gz |
Install setuptools before install GCAP. To avoid python version conflicts, users are recommended to use virtualenv.
Install GCAP:
git clone https://github.com/qinqian/GCAP
cd GCAP
## fill in your gcap.conf in the directory and add species section like [hg19], [mm9], [hg38], [mm10]
python setup.py install
Pair End Usage:
GCAP -i "test_pair2.fastq,test_pair1.fastq;test_pair2.fastq,test_pair1.fastq" -n test -o test -s hg19 --pe --threads 18
Single End Usage:
GCAP -i test.fastq,test.fastq -n test -o test -s hg19 --threads 10
Outputs from GCAP
QC metrics stored files in one json summary
- test treat rep1 readquality totalreads mapped FragmentSize PBC1 NSC spot broadPeaknum narrowPeaknum UniquePosRatio
- test treat rep2 readquality totalreads mapped UniquePosRatio NSC spot broadPeaknum narrowPeaknum FragmentSize PBC1
- correlation between replicates
- overlap divided by union_bases of peaks
- mergedBroadPeak number
- mergedNarrowPeak
