ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline

ENCODE-DCC/atac-seq-pipeline Issues

How to set the seed when subsampling reads
Updated a month ago1
build_genome_sh did not finish running
Updated 3 months ago
Running without external network connection
Updated 3 months ago5
Discrepancy between signal p-value and fold change bigwig tracks around the open regions
Updated 3 months ago
If the pipeline can be used when data is from other platforms (eg: DNBSEQ-G400).
Updated 4 months ago1
bam files with replicates
Updated 4 months ago1
Differences in qc when validating installation
Closed 5 months ago3
Don't need to trim adapters
Closed 5 months ago
Add --ntasks-per-node or --exclusive option for your multi-process jobs.
Updated 6 months ago
Failed on fastqs having identical filename but different path
Updated 6 months ago3
The pipeline stalled at "chip.read_genome_tsv" for local backend
Updated 7 months ago2
Confirming that separate conditions/treatments should be analyzed by separate pipelines
Closed 7 months ago2
Interpreting result files and selecting files for visualization and DAR analysis
Closed a year ago4
'mm10_no_alt_analysis_set_ENCODE.fasta.gz.lock' could not be acquired
Updated 8 months ago2
Memory Saving: too many large files?
Updated 10 months ago
[Question]: Do reads need to be deduped before FRiP calculation
Closed 10 months ago6
--read-len selection
Updated 10 months ago
two replicates and the combined have different signal
Updated 10 months ago
More than 10 replicates
Updated 10 months ago3
Invalid MEMLIMIT unit value with LSF jobs on Linux
Updated 10 months ago
Encode-atac-seq-pipeline environment can't be found?
Updated 10 months ago
Duplicated reproducible peaks
Updated 10 months ago4
6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
Updated a year ago
Help with running the pipeline
Updated a year ago1
Unable to run the pipeline. invalid jar file error
Updated a year ago3
Reuse the same files in case of error.
Updated a year ago
Build genome database for your own genome and
Updated a year ago6
Finished parsing without consuming all tokens
Updated a year ago1
How are DNAse-seq data processed with this pipeline?
Updated a year ago
How are mitochondrial reads aligned?
Updated a year ago1
test JSON timing out.
Updated a year ago3
What should I cite
Updated a year ago
AttributeError: module 'grpc' has no attribute '__version__'
Closed a year ago1
Multi-architecture docker image
Updated a year ago
pipeline because javax.net.ssl.SSLException failed
Updated a year ago1
Pipeline Fails at Peak Calling
Updated a year ago1
Job atac.align:0:2 exited with return code 3
Updated a year ago4
Pipeline is stuck on atac.read_genome_tsv:-1 on HPC
Closed a year ago1
configparser.NoSectionError: No section: 'defaults'
Updated 2 years ago1
How do I use IGV to visualize the ATAC peak result
Updated 2 years ago1
conda install fails
Closed 2 years ago3
caper init lsf not supported
Updated 2 years ago1
ERROR when Validating WDL/inputs/imports with Womtool
Updated 2 years ago3
How to deal with repeat peaks in idr.optimal_peak.narrowPeak
Closed 2 years ago2
Error Running Analysis on DNAnexus Platform (web)
Updated 2 years ago
Cannot access sample_R1.trim.srt.bam or sample_R1.trim.srt.no_chrM.samstats.qc: No such file or directory
Closed 2 years ago2
Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!
Closed 2 years ago2
Build Genome Database stuck on ebwt loop
Updated 2 years ago
unable to install hg38
Updated 2 years ago1
Meaning of "fold change over control" in ATAC-seq output
Closed 2 years ago4