| 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” |
2 Explanation of variables
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
3 Total reads
3.1 Read Quality
3.2 Read assignment
3.3 Edits
4 Reads by barcode
5 Summary Table
| 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