ENCODE-DCC atac-seq-pipeline issues

ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline

MIT License

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issues

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Obtaining main outputs from WDL runners other than Cromwell?

#450 adamnovak opened 2 weeks ago
0
Building Custom Genome Instructions

#449 imk1 opened 2 weeks ago
0
About define promoter region from gencode.gtf file

#448 GleeenSIBS opened 3 weeks ago
0
Pipeline Processing Only First Two Samples in Metadata

#447 achisha21 opened 1 month ago
0
Leader job attempts to run non-existent shell script

#446 sbresnahan opened 1 month ago
0
Can NOT install the software.

#445 shaohuaihan opened 2 months ago
0
Fix last read output

#444 chenminicode opened 2 months ago
0
Failure at atac.read_genome_tsv

#443 shk44 opened 2 months ago
0
Pipeline stuck

#442 JaskaranNeuro opened 2 months ago
0
How to set the seed when subsampling reads

#441 Al-Murphy opened 4 months ago
1
build_genome_sh did not finish running

#440 Glinland opened 6 months ago
2
Discrepancy between signal p-value and fold change bigwig tracks around the open regions

#439 AayushGrover opened 6 months ago
0
If the pipeline can be used when data is from other platforms (eg: DNBSEQ-G400).

#438 lillianj97 opened 6 months ago
1
bam files with replicates

#437 moshe-olshansky opened 7 months ago
1
v2.2.3

#436 leepc12 closed 7 months ago
0
WRN-503

#435 leepc12 closed 7 months ago
0
Add --ntasks-per-node or --exclusive option for your multi-process jobs.

#434 feather-W opened 8 months ago
0
Don't need to trim adapters

#433 feather-W closed 8 months ago
0
Confirming that separate conditions/treatments should be analyzed by separate pipelines

#432 OrangeyO2 closed 10 months ago
2
Failed on fastqs having identical filename but different path

#431 yunhailuo opened 11 months ago
3
Differences in qc when validating installation

#430 bozidar-obradovic closed 8 months ago
3
The pipeline stalled at "chip.read_genome_tsv" for local backend

#429 erhei01 opened 1 year ago
2
Memory Saving: too many large files?

#428 Rafaelsoler13 opened 1 year ago
0
--read-len selection

#427 songxh1996 opened 1 year ago
0
two replicates and the combined have different signal

#426 HYan-lei opened 1 year ago
0
Invalid MEMLIMIT unit value with LSF jobs on Linux

#425 skoplev opened 1 year ago
1
[Question]: Do reads need to be deduped before FRiP calculation

#424 tamuanand closed 1 year ago
6
Encode-atac-seq-pipeline environment can't be found?

#423 riteshkc opened 1 year ago
0
More than 10 replicates

#422 LinearParadox opened 1 year ago
3
6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running

#421 marlmatos opened 1 year ago
0
Unable to run the pipeline. invalid jar file error

#420 Shashankti opened 1 year ago
3
Help with running the pipeline

#419 Chrisdoan9 opened 1 year ago
1
Reuse the same files in case of error.

#418 Rafaelsoler13 opened 1 year ago
0
How are DNAse-seq data processed with this pipeline?

#417 sufyazi opened 1 year ago
0
How are mitochondrial reads aligned?

#416 imk1 opened 1 year ago
1
Finished parsing without consuming all tokens

#415 LI-Qinyao opened 1 year ago
1
Build genome database for your own genome and

#414 Rafaelsoler13 opened 1 year ago
7
Interpreting result files and selecting files for visualization and DAR analysis

#413 Rafaelsoler13 opened 1 year ago
4
What should I cite

#412 Al-Murphy opened 1 year ago
0
AttributeError: module 'grpc' has no attribute '__version__'

#411 Rafaelsoler13 closed 1 year ago
1
Multi-architecture docker image

#410 jwtobias opened 1 year ago
0
pipeline because javax.net.ssl.SSLException failed

#409 sjh996 opened 1 year ago
1
Pipeline Fails at Peak Calling

#408 arianraje opened 1 year ago
1
Duplicated reproducible peaks

#407 satroz opened 1 year ago
4
Job atac.align:0:2 exited with return code 3

#406 icen234 opened 1 year ago
4
v2.2.2

#405 leepc12 closed 1 year ago
0
fix zero len for tn5 shifting

#404 leepc12 closed 1 year ago
0
Running without external network connection

#403 FrancoisMifsud opened 1 year ago
5
Pipeline is stuck on atac.read_genome_tsv:-1 on HPC

#402 danielcasto closed 1 year ago
1
configparser.NoSectionError: No section: 'defaults'

#401 mingjianPeng opened 1 year ago
1