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databio
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pepatac
A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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Incorrectly reported number of duplicates
#150
gbloeb
closed
4 years ago
2
Warning about genome assets
#149
gbloeb
closed
4 years ago
13
Remove duplicates first or filter low mapping quality first?
#148
yangmqglobe
closed
3 years ago
1
peak reduce script can't not get output file arg property
#147
yangmqglobe
closed
4 years ago
1
peak reduce script can't not get output file arg property
#146
yangmqglobe
closed
4 years ago
0
add bwa option for aligner
#145
nsheff
closed
4 years ago
1
Bigwig track normalized or not?
#144
Zhuxitong
closed
4 years ago
3
Dev
#143
jpsmith5
closed
4 years ago
0
File not found during bowtie2 step
#142
hugokitano
closed
4 years ago
2
Release 0.9.0
#141
nsheff
closed
4 years ago
0
pep 2.0 to dev
#140
nsheff
closed
4 years ago
0
invalid Project.looper.output_dir reference
#139
stolarczyk
closed
4 years ago
6
Alignment fails if no prealignments are specified
#138
nsheff
closed
4 years ago
2
switch to new refgenconf path retrieval strategy
#137
stolarczyk
closed
4 years ago
0
update cfg2 with dev changes
#136
nsheff
closed
4 years ago
0
bulker problem with bedToBigBed
#135
jpsmith5
closed
4 years ago
3
macs2 error
#134
nsheff
closed
4 years ago
3
make bamqc less verbose
#133
nsheff
closed
4 years ago
1
alignment repeats
#132
nsheff
closed
4 years ago
5
command_template
#131
nsheff
closed
4 years ago
0
checks are outdated
#130
nsheff
closed
4 years ago
1
refgenconf object type is changed by attmap
#129
nsheff
closed
4 years ago
3
Missing refgenie assets
#128
nsheff
closed
4 years ago
5
Updating to refgenie
#127
nsheff
closed
4 years ago
2
TypeError: descriptor 'splitlines' requires a 'str' object but received a 'unicode'
#126
mbardus
closed
4 years ago
2
Object arrays cannot be loaded when allow_pickle=False
#125
mbardus
closed
4 years ago
0
pararead import error
#124
mbardus
closed
4 years ago
1
cannot complete image building with "make docker"
#123
DzLGasoline
closed
5 years ago
2
ModuleNotFoundError: No module named 'pypiper'
#122
qiaowei-vvjoe
closed
4 years ago
9
Siphoning off Alu repeats
#121
juheon
closed
4 years ago
1
clone GitHub repositories with HTTPS
#120
fhalbritter
closed
4 years ago
1
bamSitesToWig asking for non-integer number of cores
#119
rcorces
closed
4 years ago
4
Fix #116.
#118
nsheff
closed
4 years ago
0
Merge bam files for duplicates prior to calling peaks
#117
sthair
closed
4 years ago
1
OSError: [Errno 5] Input/output error: 'lock.stats.tsv'
#116
dearxxj
closed
5 years ago
18
Problem expanding $REFGENIE env var
#115
jpsmith5
closed
5 years ago
17
Insert size distribution
#114
sthair
closed
4 years ago
3
MACS2 customization
#113
sthair
closed
5 years ago
10
Output BAMs have incomplete @RG line in header
#112
rcorces
closed
4 years ago
5
Use RGC
#111
vreuter
closed
5 years ago
3
singularity usage docs?
#110
vreuter
closed
5 years ago
2
streamline what reads files we keep
#109
nsheff
closed
4 years ago
1
eliminating tools dependencies
#108
nsheff
closed
4 years ago
1
commands running on repeated pipeline run
#107
nsheff
closed
4 years ago
1
Docs
#106
nsheff
closed
5 years ago
0
core number calculation needs to force an int result (python3)
#105
stolarczyk
closed
5 years ago
2
indentation problem leading to missing TssEnrichment.txt
#104
stolarczyk
closed
5 years ago
2
test example failure; ValueError
#103
stolarczyk
closed
5 years ago
5
'custom annotation' wording is overloaded
#102
nsheff
closed
4 years ago
0
summary demo links images are missing
#101
nsheff
closed
4 years ago
1
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