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QC R scripts

Following R scripts can be found at github.com/PacificBiosciences/barcoding/scripts/r. Ensure that all R dependencies are installed

install.packages(c("ggplot2","dplyr","tidyr","viridis","scales","data")) ## report_detail.R

The first is for the lima.report file: report_detail.R. Example:

$ Rscript --vanilla report_detail.R prefix.lima.report

The second, optional argument is the output file type png or pdf, with png as default:

$ Rscript --vanilla report_detail.R prefix.lima.report pdf

You can also restrict output to only barcodes of interest, using the barcode name not the index. For example, all barcode pairs that contain the barcode “bc1002”:

$ Rscript --vanilla report_detail.R prefix.lima.report png bc1002

A specific barcode pair “bc1020–bc1045”; note that, the script will look for both combinations “bc1020–bc1045” and “bc1045–bc1020”:

$ Rscript --vanilla report_detail.R prefix.lima.report png bc1020--bc1045

Or any combination of those two:

$ Rscript --vanilla report_detail.R prefix.lima.report pdf bc1002 bc1020--bc1045 bc1321

Yield

Per-barcode base yield:

Per-barcode read yield:

Per-barcode ZMW yield:

Scores

Score per number of adapters (lines) and all adapters (histogram). #What are half adapters?

Read length vs. mean score (99.9% percentile)

HQ length vs. mean score (99.9% percentile)

Read length (99.9% percentile, 1000 binwidth)

Grouped by barcode, same y-axis :

Grouped by barcode, free y-axis:

Not grouped into facets, line histogram:

Barcoded vs. non-barcoded:

HQ length (99.9% percentile, 2000 binwidth)

Grouped by barcode, same y-axis:

Grouped by barcode, free y-axis:

Not grouped into facets, line histogram:

Barcoded vs. non-barcoded:

Adapters (99.9% percentile, 1 binwidth)

Number of adapters:

report_summary.R

The second script is for high-plex data in one lima.report file: report_summary.R.

Example:

$ Rscript --vanilla report_summary.R prefix.lima.report

Yield per barcode:

Score distribution across all barcodes:

Score distribution per barcode:

Read length distribution per barcode:

HQ length distribution per barcode:

Bad adapter ratio histogram:


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