8.1 Set Up Executions

Steps

1. Select Workflows from the left sidebar, then select INDUCE-seq.

2. Under Sample Manifest Input, configure the sample manifest:

   • Under Sample Manifest Type, select Registry Sample Manifest, then Import Rows from Registry.
   • Navigate to your sample manifest, then select Next.
   • Select the samples to include in the run, then select Next. Use the checkbox to the left of the sample column to select all samples.
   • Confirm that the workflow parameter column names match the sample manifest column names.
   • Select Import.

3. Under Nuclease Manifest Input, configure the nuclease manifest:

   • Under Nuclease Manifest Type, select Registry Nuclease Manifest, then Import Rows from Registry.
   • Navigate to your nuclease manifest, then select Next.
   • Select the nuclease mechanisms to include, then select Next.
   • Confirm that the workflow parameter column names match the nuclease manifest column names.
   • Select Import.

4. Select the sequencing platform used for the sequencing run.

5. Select a reference genome:

   Standard Reference GenomeCustom Genome

   Toggle the button and select from hg19, hg38, or t2t.

   

   Upload the following files to the LatchBio Data tab before proceeding (mounting an AWS or GCP bucket is recommended):

   File	Format	Required?
   BWA Index Directory	Directory containing the genome indexed with bwa index	Required
   Custom genome sequence	FASTA format	Required
   Chromosome Sizes	BED file: chr.. 0 chromosome_length	Required
   Gene Annotations	BED file: chr.. start end gene_name	Optional
   Repeat Mask	BED file: chr.. start end repeat_name	Optional
   Exclude List	BED file: chr.. start end — must have suffix .excludelist.bed	Optional

   Warning

   Contig names in the genome must start with chr.

   

6. Under Output Parameters, select Select Folder and choose an output folder for results. For recommended folder organisation, see Example Folder Structure.

7. Enter an execution name. Only alphanumeric characters, underscores (_), and hyphens (-) are permitted. Date and time are added automatically.

8. Configure Advanced Parameters (optional):

   Read Filtering

   • Minimum read threshold: Minimum number of reads required for inclusion in downstream analysis.
   • MAPQ threshold: Default removes reads with MAPQ below 30. Can be lowered to retain reads in repetitive regions where MAPQ values may fall below the default. Lowering below the default is generally not recommended as it increases false-positive risk.
   ExAmp / Optical Duplicate Parameters

   • Duplicate detection distance: Detection distances have been increased to match the NextSeq 2000 flow cell characteristics. Override with clumpify_dupedist and markdup_dist parameters if required.
   • ExAmp duplicate filtering: Optional step to increase ExAmp duplicate artefact removal stringency. Non-reproducible single-stranded sites are excluded by default when enabled. The minimum break count for site removal at this step is configurable (default: 5).

9. Select Launch Workflow to start the run.