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6.1 Import Sample Manifest File

Each row of the sample manifest represents a different sample or sample replicate.

Warning

Sample names must match FASTQ prefix names exactly. A mismatch will cause the INDUCE-seq Analysis to fail.

Manifest column reference

Column Description Required? Example
sample Sample name. Must match the FASTQ prefix exactly. No spaces or periods. Required Cas9_PDCD1_24h_rep1
nuclease_mechanism Name of the nuclease mechanism from the nuclease manifest. Leave blank for untreated controls. Required cas9_PDCD1
condition Groups replicates and labels samples in output reports. For treated samples, this value is used to associate them with controls. Include all information needed to identify the sample group. Required control_Cas9_4h
control Enter control for control samples. For treated samples, enter the condition value of the associated control. Required control
fastq_1 Path to the Read 1 FASTQ file. Do not edit — populated in the Connect Your FASTQs step. — —
fastq_2 Path to the Read 2 FASTQ file. Do not edit — populated in the Connect Your FASTQs step. — —
breakends Path to the breakends file from a previous run. Do not edit unless re-running samples to combine experiments or reduce run time. — —
gDNA_yield_ng Amount of gDNA extracted per sample (ng). Optional 1002
library_yield_ng Library yield per sample (ng). Optional 374
qPCR_conc_pM Library concentration available for sequencing (pM). Optional 1.46

Steps

  1. Navigate to your new sample manifest.
  2. Select Export, then Export View as CSV.
  3. Open the exported file in your external software.
  4. Enter the required columns and any optional columns needed. Use the horizontal scroll bar to view all columns. Refer to Example Manifest Data for a visual representation.
  5. Save the CSV file.
  6. In the BSB INDUCE-seq Analysis Workspace, navigate back to the sample manifest.
  7. Select Import, then Import from File.
  8. Navigate to the folder containing your experiment data and select Upload Files.
  9. Select your file and choose Open, or drag the file into the dialog box.
  10. Select your uploaded file, then select Select.
  11. Confirm that the CSV column names match the manifest column names in the Workspace.
  12. Select Submit. The Workspace populates the manifest with your uploaded data.