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88 Open 227 Closed
88 Open 227 Closed
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Issues list

Cannot use qvalue when call peaks with MACS2
#452 opened Nov 23, 2024 by lingyunsong
can’t create hard link
#451 opened Nov 11, 2024 by llm98m
Obtaining main outputs from WDL runners other than Cromwell?
#450 opened Sep 17, 2024 by adamnovak
Building Custom Genome Instructions
#449 opened Sep 16, 2024 by imk1
About define promoter region from gencode.gtf file
#448 opened Sep 6, 2024 by DontCareYaYa
Pipeline Processing Only First Two Samples in Metadata
#447 opened Aug 29, 2024 by achisha21
Leader job attempts to run non-existent shell script
#446 opened Aug 22, 2024 by sbresnahan
2
Can NOT install the software.
#445 opened Jul 23, 2024 by shaohuaihan
Failure at atac.read_genome_tsv
#443 opened Jul 14, 2024 by shk44
Pipeline stuck
#442 opened Jul 5, 2024 by JaskaranNeuro
How to set the seed when subsampling reads
#441 opened May 18, 2024 by Al-Murphy
1
build_genome_sh did not finish running
#440 opened Mar 26, 2024 by Glinland
2
Discrepancy between signal p-value and fold change bigwig tracks around the open regions
#439 opened Mar 15, 2024 by AayushGrover
If the pipeline can be used when data is from other platforms (eg: DNBSEQ-G400).
#438 opened Mar 7, 2024 by lillianj97
1
bam files with replicates
#437 opened Feb 26, 2024 by moshe-olshansky
1
Add --ntasks-per-node or --exclusive option for your multi-process jobs.
#434 opened Jan 10, 2024 by feather-W
Failed on fastqs having identical filename but different path
#431 opened Nov 3, 2023 by yunhailuo
3
The pipeline stalled at "chip.read_genome_tsv" for local backend
#429 opened Sep 7, 2023 by erhei01
2
Memory Saving: too many large files?
#428 opened Sep 7, 2023 by Rafaelsoler13
--read-len selection
#427 opened Sep 1, 2023 by songxh1996
two replicates and the combined have different signal
#426 opened Aug 28, 2023 by HYan-lei
Invalid MEMLIMIT unit value with LSF jobs on Linux
#425 opened Aug 22, 2023 by skoplev
3
Encode-atac-seq-pipeline environment can't be found?
#423 opened Aug 18, 2023 by riteshkc
More than 10 replicates
#422 opened Aug 12, 2023 by LinearParadox
3
6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
#421 opened Aug 7, 2023 by marlmatos
ProTip! no:milestone will show everything without a milestone.