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+| title: ‘Summary Read Report’ | +
| author: ‘ampliCan’ | +
| date: ‘17 September 2021’ | +
| output: | +
| html_document: | +
| toc: true | +
| theme: paper | +
| toc_float: true | +
| number_sections: true | +
| params: | +
| barcode_summary: “/tmp/tmp4obcv1no/job_working_directory/000/6/working/output_folder/barcode_reads_filters.csv” | +
| config_summary: “/tmp/tmp4obcv1no/job_working_directory/000/6/working/output_folder/config_summary.csv” | +
| links: “1. Report by id | +
| 2. Report by barcode | +
| 3. Report by group | +
| 4. Report by guide | +
| 5. Report by amplicon” | +
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+1 Other Reports
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+2 Explanation of variables
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Experiment Count - how many IDs belongs to this barcode
+Read Count - how many reads belongs to this barcode
+Bad Base Quality - how many reads had base quality worse than specified (default is 0)
+Bad Average Quality - how many reads had average base quality worse than specified (default is 0)
+Bad Alphabet - how many reads had alphabet with bases other than A, C, G, T
+Filtered Read Count - how many reads were left after filtering
+Unique Reads - how many reads (forward and reverse together) for this barcode is unique
+Assigned Reads/Unassigned Reads - how many reads have been assigned/not assigned to any of the experiments
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+3 Total reads
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+3.1 Read Quality
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+3.2 Read assignment
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+3.3 Edits
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+4 Reads by barcode
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+5 Summary Table
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| Barcodes | +Experiment Count | +Read Count | +Bad base quality | +Bad average quality | +Bad alphabet | +Good Reads | +Unique Reads | +Unassigned Reads | +Assigned Reads | +
|---|---|---|---|---|---|---|---|---|---|
| barcode_1 | +2 | +20 | +0 | +0 | +3 | +17 | +10 | +3 | +7 | +
| barcode_2 | +3 | +21 | +0 | +0 | +0 | +21 | +9 | +0 | +9 | +
Table 1. Reads distributed for each barcode
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