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ENCODE-DCC
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chip-seq-pipeline2
ENCODE ChIP-seq pipeline
MIT License
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Can chip-seq-pipeline2 run locally without internet?
#306
cyz0315
opened
3 days ago
0
Datasets for TF-target genes
#305
yiqisu
opened
3 months ago
0
v2.2.2
#304
leepc12
closed
4 months ago
0
WRN-503
#303
leepc12
closed
4 months ago
0
pipeline stuck in call-macs2_signal_track_pooled
#302
cmf1997
opened
5 months ago
0
How do you resume ?
#301
olechnwin
opened
8 months ago
0
missing slurm qos parameter
#300
giardine
opened
8 months ago
2
how to create pseudo-replicate files
#299
songxh1996
opened
9 months ago
1
Does the calculation of sval in encode_task_macs2_signal_track_chip.py take into account the difference between single-end and paired-end data?
#298
ezioljj
opened
10 months ago
2
signal track height is higher for input control
#297
jamesaliba
opened
1 year ago
1
no motif output
#296
jamesaliba
opened
1 year ago
0
The pipeline stops at Job chip.read_genome_tsv
#295
peculiar97
opened
1 year ago
10
Fixed peak size
#294
kbattenb
opened
1 year ago
1
”caper init local“ error
#293
songxh1996
opened
1 year ago
3
caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
#292
Ritetsu
opened
1 year ago
1
Changing MACS2 output from earlier pipeline version
#291
clarabakker
opened
1 year ago
2
Error in Alignment process : Call input and runtime attributes evaluation failed for align: Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size
#290
cafri1105
closed
1 year ago
2
No peak call output from "TF" pipeline
#289
jsemple19
closed
1 year ago
4
caper.wdl_parser|ERROR| Failed to parse WDL with miniwdl.
#288
wbszhu
closed
1 year ago
2
v2.2.1
#287
leepc12
closed
1 year ago
0
Hotfix conda support
#286
leepc12
closed
1 year ago
0
Conflicts while running scripts/install_conda_env.sh
#285
agduncan94
opened
1 year ago
3
HELP: call-xcor fails with TEST command
#284
yinyeya
opened
2 years ago
3
Are adapter-trimmed FASTQs required?
#283
benayang
opened
2 years ago
3
v2.2.0
#282
leepc12
closed
2 years ago
0
Pipe 77 shorten conda env name
#281
leepc12
closed
2 years ago
0
Where are the peak files from MACS2 output stored?
#280
gene-drive
opened
2 years ago
0
Problem about build_genome_data.sh
#279
Mozillian1
closed
1 year ago
2
Terra output missing metadata.json
#278
elisadonnard
opened
2 years ago
1
can this wdl pipeline be run with cromwell engine?
#277
gudeqing
opened
2 years ago
0
Pipeline stalls before IDR steps
#276
gene-drive
opened
2 years ago
3
hotfix fix py2 shebang
#275
leepc12
closed
2 years ago
0
Hotfix py2 in filter task
#274
leepc12
closed
2 years ago
0
Advice on output folders/files
#273
gene-drive
closed
2 years ago
1
Issue with running tf file
#272
shirleytemples
opened
2 years ago
6
|ERROR| Failed to parse WDL with miniwdl, |ERROR| Conda environment name not found in WDL metadata
#271
shirleytemples
closed
2 years ago
1
v2.1.5
#270
leepc12
closed
2 years ago
0
fix spp multithreading bug
#269
leepc12
closed
2 years ago
0
parrallel proccessing with spp
#268
louisgevirtzman
closed
2 years ago
2
Pipe 48 fix broken conda dependency
#267
leepc12
closed
2 years ago
0
Run gives error
#266
shirleytemples
closed
2 years ago
12
TEST run gave an error. Please help!
#265
yingsun-ucsd
closed
2 years ago
6
v2.1.4
#264
leepc12
closed
2 years ago
0
more info in qc_report
#263
leepc12
closed
2 years ago
0
Pip 1667 fix conda conflicts
#262
leepc12
closed
2 years ago
0
call-xcor fails before peak calling
#261
wx2022
closed
2 years ago
4
A question about the use of fragment length estimated from cross-correlation analysis.
#260
yr-gh
closed
2 years ago
0
cc.plot.png, cc.fraglen, no such file or directory
#259
shirleytemples
closed
2 years ago
5
Unable to run caper on windows
#258
silentsilencee
closed
2 years ago
3
caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/net/waterston/vol2/home/gevirl/chip-seq-pipeline2-2.1.2/chip.wdl
#257
louisgevirtzman
opened
2 years ago
8
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