nrhorner
commented
3 months ago Hi @jackchenx3
The workflow identifies chimeric reads, those with 2 or more sub-reads fused into a single read, and splits them into sub-reads. The number of reads reported in the report summary is the total number of sub-reads. This should be made more obvious in the report or workflow docs.
Thanks,
Neil
jackchenx3
Operating System
CentOS 7
Other Linux
No response
Workflow Version
2.1.0
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
No response
Workflow Execution - CLI Execution Profile
None
What happened?
Hi,
I'm using the latest version (2.1.0) to process my ONT single-cell data and noticed a discrepancy between the number of reads in the input FASTQ file and those reported in the HTML file. My FASTQ file contains 83,602,375 reads, but the HTML report shows 84,827,979 input reads. This issue also occurred in the previous version of the wf-single-cell pipelines, where the HTML report consistently shows 1-2% more input reads across all the samples I've processed.
I'm curious to know at which step in the process the input FASTQ file is counted and how the input read number is determined.
Thanks
Jack
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response