snystrom / cutNrun-pipeline

Analysis pipeline for CUT&RUN Data. Currently configured for use in the McKay Lab at UNC, but extensible elsewhere by changing configuration files.

snystrom/cutNrun-pipeline Issues

zNormalization
Updated a year ago2
spike-in normalization of bigwigs fails miserably
Closed 2 years ago8
Stop calling MACS2 peaks from ControlDNAPath. Use sample-specific inputs, or MACS default background adjustments.
Closed 5 years ago33
Add FrIP score computation
Updated 4 years ago
Alignment stats & genome info stats don't compute at each filtering step
Updated 4 years ago
alignmentStats rules are broken
Closed 4 years ago
envmodules not compatible with run commands
Updated 4 years ago1
Environment Modules (new snakemake version feature)
Updated 4 years ago1
Fix Readme
Closed 4 years ago1
bed files have unusual fragment size distributions
Closed 4 years ago1
Allow normalization to arbitrary number of genomes
Closed 4 years ago1
Use IDR for pooled peak assessment
Closed 4 years ago1
add bbsplit step
Closed 4 years ago1
Spike-in using combined genome
Closed 4 years ago1
Combine bedgraph -> bigwig steps
Updated 4 years ago
adapter trimming needs modification
Closed 4 years ago1
Allow sample-specific negative control
Updated 4 years ago1
make fragment size distribution plots
Updated 4 years ago3
QC Metrics & Report
Updated 4 years ago1
Make dashboard-style summary plot for each sample
Updated 4 years ago2
Do not include file paths that don't exist in sampleSheet output
Updated 4 years ago
Ignore test/ directory in multiqc step
Updated 4 years ago
fix .gitignore to not ignore sampleInfo, do ignore raw data
Updated 4 years ago1
ignore test/ directory during multiqc step
Updated 5 years ago
check for valid genomes
Updated 5 years ago
reduceFastqScreen threads
Closed 5 years ago
Check that baseNameCols exist in sampleInfo.tsv
Updated 5 years ago
Set `readLen` in sample-specific way
Updated 5 years ago
use config.json to pass parameters instead of snakefile header
Closed 5 years ago
Add columns for final output files to sampleSheet & pooledSampleSheet
Closed 5 years ago
noYUHet
Closed 5 years ago
FragType & NormType aren't correctly detected
Updated 5 years ago2
Add FastqScreen step
Closed 5 years ago1
merge techincal replicates in sample sheet
Closed 5 years ago
remove --extsize from MACS peak calling
Closed 5 years ago
Aggregate all fastqscreen.txt outputs into single summary table, make final output plot
Updated 5 years ago
Define `threads` in config file
Updated 5 years ago
add rules to make pooled files
Updated 5 years ago
add frag-size dist histogram
Closed 5 years ago
Make sampleSheet & poolSampleSheet outputs within a rule
Updated 5 years ago
set -e in snakemake so stderr and stdout go to different places
Closed 5 years ago
add threshold peak calling
Closed 6 years ago
make bg files temp()
Closed 6 years ago
Don't keep Sam output?
Updated 6 years ago