Skip to content

Issues: ENCODE-DCC/atac-seq-pipeline

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

88 Open 227 Closed
88 Open 227 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

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! Adding no:label will show everything without a label.