snystrom cutNrun-pipeline issues

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.

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issues

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zNormalization

#46 mniederhuber opened 1 year ago
2
Add SEACR peak-calling functionality

#45 half-adder closed 2 years ago
2
spike-in normalization of bigwigs fails miserably

#44 snystrom closed 1 year ago
8
Add FrIP score computation

#43 snystrom opened 3 years ago
0
Alignment stats & genome info stats don't compute at each filtering step

#42 snystrom opened 3 years ago
0
Update README.md

#41 mniederhuber closed 3 years ago
1
envmodules not compatible with run commands

#40 snystrom opened 3 years ago
1
alignmentStats rules are broken

#39 snystrom closed 3 years ago
0
Spike-in using combined genome

#38 snystrom closed 3 years ago
1
Combine bedgraph -> bigwig steps

#37 snystrom opened 3 years ago
0
adapter trimming needs modification

#36 snystrom closed 3 years ago
1
Do not include file paths that don't exist in sampleSheet output

#35 snystrom opened 3 years ago
0
Ignore test/ directory in multiqc step

#34 snystrom opened 3 years ago
0
fix .gitignore to not ignore sampleInfo, do ignore raw data

#33 snystrom opened 3 years ago
1
add bbsplit step

#32 snystrom closed 3 years ago
1
Allow sample-specific negative control

#31 snystrom opened 4 years ago
1
ignore test/ directory during multiqc step

#30 snystrom opened 4 years ago
0
Stop calling MACS2 peaks from ControlDNAPath. Use sample-specific inputs, or MACS default background adjustments.

#29 snystrom closed 4 years ago
33
check for valid genomes

#28 snystrom opened 4 years ago
0
reduceFastqScreen threads

#27 snystrom closed 4 years ago
0
Check that baseNameCols exist in sampleInfo.tsv

#26 snystrom opened 4 years ago
0
Set `readLen` in sample-specific way

#25 snystrom opened 4 years ago
0
Aggregate all fastqscreen.txt outputs into single summary table, make final output plot

#24 snystrom opened 4 years ago
0
Define `threads` in config file

#23 snystrom opened 4 years ago
0
Environment Modules (new snakemake version feature)

#22 snystrom opened 4 years ago
1
Add FastqScreen step

#21 snystrom closed 4 years ago
1
Use IDR for pooled peak assessment

#20 snystrom closed 3 years ago
1
Make dashboard-style summary plot for each sample

#19 snystrom opened 4 years ago
2
make fragment size distribution plots

#18 snystrom opened 4 years ago
3
Fix Readme

#17 snystrom closed 3 years ago
1
Make sampleSheet & poolSampleSheet outputs within a rule

#16 snystrom opened 4 years ago
0
Allow normalization to arbitrary number of genomes

#15 snystrom closed 3 years ago
1
use config.json to pass parameters instead of snakefile header

#14 snystrom closed 4 years ago
0
bed files have unusual fragment size distributions

#13 snystrom closed 3 years ago
1
QC Metrics & Report

#12 snystrom opened 4 years ago
1
FragType & NormType aren't correctly detected

#11 snystrom opened 5 years ago
2
add threshold peak calling

#10 snystrom closed 5 years ago
0
remove --extsize from MACS peak calling

#9 snystrom closed 4 years ago
0
set -e in snakemake so stderr and stdout go to different places

#8 snystrom closed 4 years ago
0
add frag-size dist histogram

#7 snystrom closed 4 years ago
0
make bg files temp()

#6 snystrom closed 5 years ago
0
merge techincal replicates in sample sheet

#5 snystrom closed 4 years ago
0
noYUHet

#4 snystrom closed 4 years ago
0
Don't keep Sam output?

#3 snystrom opened 5 years ago
0
Add columns for final output files to sampleSheet & pooledSampleSheet

#2 snystrom closed 4 years ago
0
add rules to make pooled files

#1 snystrom opened 5 years ago
0