what's the input summary in your config.yaml?

nanoporetech / DTR-phage-pipeline

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what's the input summary in your config.yaml? #3

Closed zhanwen-cheng closed 4 years ago

zhanwen-cheng commented 4 years ago

Hi, what's the 'input_summary' in your 'config.yaml'? Is this the 'sequencing_summary.txt' you got after basecalling?

jmeppley commented 4 years ago

That is correct. It should be a text table with one row per read with a header line like this:

filename_fastq  filename_fast5  read_id run_id  channel mux     start_time
     duration        num_events      passes_filtering        template_start
 num_events_template     template_duration   sequence_length_template
 mean_qscore_template    strand_score_template   median_template
mad_template    pore_type       experiment_id   sample_id

-John