Hello, I'm trying to run ENCODE ChIP-Seq pipeline by shell commands step-by-step picked up from your Python scripts instead of installing your pipeline. But I have a question about the use of fragment length estimated by cross-correlation analysis.
I don't know which replicate FASTQ file (I have two biological replicates) should be trimmed to 50bp, then run by cross-correlation analysis to get the estimated fragment length. And which estimated fragment length (At present, I estimate fragment length for both biological replicates) should be used for downstream peak calling. Because I have 9 tagAlign files (Rep1, Rep2, Pooled, and their pr1/2) to be called.
I'm really grateful for your help.
OS/Platform
OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
Conda version: If you used Conda ($ conda --version).
Pipeline version: [e.g. v1.6.0]
Caper version: [e.g. v1.2.0]
Caper configuration file
Paste contents of ~/.caper/default.conf.
PASTE CAPER CONF CONTENTS HERE
Input JSON file
Paste contents of your input JSON file.
PASTE INPUT JSON CONTENTS HERE
Troubleshooting result
If you ran caper run without Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.
If you ran caper submit with a running Caper server then first find your workflow ID (1st column) with caper list and run caper debug [WORKFLOW_ID].
Describe the bug
Hello, I'm trying to run ENCODE ChIP-Seq pipeline by shell commands step-by-step picked up from your Python scripts instead of installing your pipeline. But I have a question about the use of fragment length estimated by cross-correlation analysis.
I don't know which replicate FASTQ file (I have two biological replicates) should be trimmed to 50bp, then run by cross-correlation analysis to get the estimated fragment length. And which estimated fragment length (At present, I estimate fragment length for both biological replicates) should be used for downstream peak calling. Because I have 9 tagAlign files (Rep1, Rep2, Pooled, and their pr1/2) to be called.
I'm really grateful for your help.
OS/Platform
$ conda --version).Caper configuration file
Paste contents of
~/.caper/default.conf.Input JSON file
Paste contents of your input JSON file.
Troubleshooting result
If you ran
caper runwithout Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.If you ran
caper submitwith a running Caper server then first find your workflow ID (1st column) withcaper listand runcaper debug [WORKFLOW_ID].Paste troubleshooting result.