Comments (2)
Hi, if necessary in your view, could you add the json file about this sample's example here slurm document situation , since after download, just get file.fastq.gz like
/my_path/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1
ENCFF106QGY.subsampled.400.fastq.gz ENCFF341MYG.subsampled.400.fastq.gz
then, next step become file.json, so how it become?
$ INPUT=examples/local/ENCSR356KRQ_subsampled.json
from atac-seq-pipeline.
input JSON (examples/local/ENCSR356KRQ_subsampled.json
) is included in this repo.
https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/examples/local/ENCSR356KRQ_subsampled.json
from atac-seq-pipeline.
Related Issues (20)
- Finished parsing without consuming all tokens HOT 1
- How are mitochondrial reads aligned? HOT 1
- How are DNAse-seq data processed with this pipeline?
- Reuse the same files in case of error.
- Help with running the pipeline HOT 1
- Unable to run the pipeline. invalid jar file error HOT 3
- 6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
- More than 10 replicates HOT 3
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- The pipeline stalled at "chip.read_genome_tsv" for local backend HOT 2
- Differences in qc when validating installation HOT 3
- Failed on fastqs having identical filename but different path HOT 3
- Confirming that separate conditions/treatments should be analyzed by separate pipelines HOT 2
- Don't need to trim adapters
- Add --ntasks-per-node or --exclusive option for your multi-process jobs.
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