epigen atacseq_pipeline issues

epigen / atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

https://epigen.github.io/atacseq_pipeline/

MIT License

47 stars 2 forks source link

issues

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Compatibility outside ATAC-seq data

#50 BiotechPedro closed 1 month ago
1
try using HOMER with conda

#49 sreichl opened 2 months ago
2
Macs2 keep dup configurable

#48 sreichl closed 2 months ago
0
make duplicate handling configurable

#47 sreichl closed 2 months ago
1
download resources directly from Zenodo

#46 sreichl opened 2 months ago
0
add Chrom Y info to docs

#45 sreichl closed 2 months ago
1
Move/Copy UROPA template in case of Module usage

#44 sreichl closed 2 months ago
1
is it necessary to copy this pipeline for each dataset?

#43 zhangzhen closed 3 months ago
1
Input files

#42 BiotechPedro closed 4 months ago
3
provide promoter_annotation.csv for downstream analyses

#41 sreichl closed 7 months ago
0
Save TSS_regions table also

#40 dariarom94 closed 7 months ago
1
remove UCSC genome browser track hub

#39 sreichl closed 7 months ago
0
Promoter beds extend the genome size

#38 dariarom94 closed 7 months ago
4
aggregated HOMER results are empty although knownResults.txt in sample results are non-empty

#37 sreichl closed 7 months ago
0
Duplicated empty rows in poromoter_counts.csv

#36 sreichl closed 7 months ago
4
make test data larger to include peaks and motifs

#35 sreichl opened 10 months ago
1
Update rulegraph to reflect latest feature additions

#34 sreichl closed 7 months ago
0
handle exception when no known motifs are found by HOMER

#33 sreichl closed 10 months ago
0
document config of UROPA

#32 sreichl closed 11 months ago
0
mitochondrial fraction metric is missing in report

#31 sreichl closed 11 months ago
0
consider including TOBIAS

#30 sreichl closed 11 months ago
1
split UROPA region annotation rule to parallelize

#29 sreichl closed 12 months ago
0
clean bash commands of all rules

#28 sreichl closed 11 months ago
0
test on ATAChom within JakStruct

#27 sreichl closed 11 months ago
1
create and add versions to all env.yaml files

#26 sreichl closed 1 year ago
0
make Snakemake 7 compatible

#25 sreichl closed 1 year ago
0
reduce scope/remove redundancy to other modules

#24 sreichl closed 1 year ago
0
simplify configuration to 2 files

#23 sreichl closed 1 year ago
1
Adapt result folder and report to MR.PARETO standard

#22 sreichl closed 1 year ago
0
revamp MultiQC report

#21 sreichl closed 12 months ago
0
resource download

#20 sreichl closed 12 months ago
0
add example (micro)data for hg38 & mm10

#19 sreichl closed 11 months ago
2
promoter region quantification

#18 sreichl closed 11 months ago
0
(automated) QC: add tutorial & tips

#17 sreichl closed 12 months ago
0
genetic sex testing functionality as QC

#16 sreichl closed 12 months ago
0
aggregate sample-wise HOMER results for downstream analyses

#15 sreichl closed 11 months ago
0
make parameter slop_extension configurable

#14 sreichl closed 1 year ago
0
make the hub shareable

#13 sreichl closed 11 months ago
4
Install Homer should be a rule/job

#12 sreichl closed 1 year ago
0
consensus region annotation file

#11 sreichl closed 12 months ago
0
Genetic similarity testing with (Picard) functionality

#10 sreichl closed 12 months ago
0
extract MultiQC statistics

#9 sreichl closed 12 months ago
0
remove tmp bam files before bowtie execution

#8 sreichl closed 12 months ago
0
consider changing consensus region generation, quantification, aggregation to R package GenomicRegions to make it more citable/understandable

#7 sreichl closed 1 year ago
0
quick aggregation of counts and support option from 4-8h to minutes

#6 sreichl closed 12 months ago
1
refactorize, reduce scope/remove redundancy to other modules and integrate into MR.PARETO for v1.0.0

#5 sreichl closed 12 months ago
0
fix multiqc.yaml installation error

#4 sreichl closed 1 year ago
0
address adapter “confusion”

#3 sreichl opened 1 year ago
2
installation error on 64-bit Ubuntu 20.04.6 LTS

#2 a-gonye closed 1 year ago
3
Building white lists

#1 descostesn closed 2 years ago
1