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Project description
CMSIP
Detecting differential 5hmC regions from CMS-IP sequencing data.
Installation
Dependencies
- bsmap
bsmap
is a component in the MOABS package. See more at MOABS (https://github.com/sunnyisgalaxy/moabs).
-
samtools: http://samtools.sourceforge.net
-
bedtools: https://bedtools.readthedocs.io
-
kentUtils: https://github.com/ENCODE-DCC/kentUtils
Example configuration file and description
sampleinfo:
- sampleid: TKO2PE1b2
group: tko
filenames:
- TKO2PE1b2_R1.fastq.gz
- sampleid: TKO2PE2m
group: tko
filenames:
- TKO2PE2b1_R1.fastq.gz
- TKO2PE2b1_R2.fastq.gz
- sampleid: WTPE1b2
group: wt
filenames:
- WTPE1b2_R1.fastq.gz
- sampleid: WTPE2b2
group: wt
filenames:
- WTPE2b2_R1.fastq.gz
groupinfo:
group1: tko
group2: wt
datainfo:
reference: hg38.fa.gz
spikein: mm10.fa.gz
windowfile: hg38_w100.bed
windowsize: 100
fastqdir: test_data
outdir: outdir
statfile: outdir/qcstats.txt
cnttablefile: outdir/meancovtable.txt.gz
ttestfile: outdir/t.test.txt
numthreads: 20
verbose: True
sampleinfo
This block stores detailed metadata information of samples.
groupinfo
This block lists the interested comparison. The alternative hypothesis is true difference in means of group1
and group2
is less than 0.
datainfo
- reference
The FASTA file for the reference genome, such as hg38.fa.gz.
- spikein
The FASTA file for the spike-in genome, such as mm10.fa.gz.
- windowfile: hg38_w100.bed
The genome in window bins. This window bin file can be generated by using bedtools. E.g.
bedtools makewindows -g <(fetchChromSizes hg38) -w 100 > hg38_w100.bed
- windowsize: 100
Window size for creating bins.
- fastqdir: test_data
Root directory with raw FASTQ files.
- outdir
Root output directory for temporary and final result files.
- statfile
QC statistics file. Default is at outdir/qcstats.txt. If this file exists, QC step will be skipped, and size factors will be parsed for the existing QC statistical file. Otherwise, QC step will run to generate the statistics file.
- cnttablefile
Region count table file. Default is at outdir/meancovtable.txt.gz. If this file exists, counting step will be skipped, and the existing count table file will be used for downstream statistical testing. Otherwise, counting step will execute to generate the count table file.
- ttestfile
The statistical testing result file. Default is at outdir/t.test.txt. If this file exists, no more task will run. Otherwise, statistical testing will run on the count table using t-test.
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