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Analysis workflow
MinKNOW acquires raw signal from the device, and sends it to the analysis pipeline (basecaller) in chunks of a defined size. Before being sent to the pipeline, MinKNOW assesses the data and determines where the individual reads start and end by detecting the abrupt signal change when DNA enters and leaves the nanopore. Only data that is considered to be within a read is sent for analysis.
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The format and location of your data will depend on the options chosen in the new experiment settings screen:
All files output directly from your experiment are located in the same directory. The directory has the structure:
{output_dir}/{experiment_id}/{sample_id}/{start_time}_{device_ID}_{flow_cell_id}_{short_protocol_run_id}/
-output_dir
is the configured output directory
-experiment_id
is the user-entered identifier for a group of runs
-sample_id
is the user-entered value for a specific sample or run. It is intended that multiple sample_ids may exist beneath an individual experiment_id
-start_time
is the time at which the protocol started in YYYYMMDD_HHMM format
-device_id
is the serial ID of the MinION Mk1B or device position for GridION/PromethION
-flow_cell_id
is the flow cell id (eg: FAH12345), either programmed on the ASIC or entered by the user
-short_protocol_run_id
is a unique identifier of 7 characters from the protocol IDExamples of the above naming convention:
/data/MyExperiment/Sample1/20181011_1759_X1_FAH12345_0ffe109
Individual read files will be split into .fast5 pass and fail folders, as well as .fastq pass and fail folder within this directory:
{flowcell_id}_{basecall_state}_{short_run_id}_{batch_number}.fastq
{flowcell_id}_{basecall_state}_{short_run_id}_{batch_number}.fast5
If the reads are barcoded, the barcode will be included in the file name before the
short_run_id
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Examples of the above file naming:fast5_pass/FAK12345_pass_9aad0448_0.fast5
fasq_pass/FAK12345_pass_9aad0448_0.fastq
Run reports can be found in the data folder (e.g. C:\data\reports).