smrtpipe.py, HGAP run - detailed description of reports generated

[Monika_bioinf]

Hello,

I would like to learn few details about the following reports from HGAP run, generated by smrtpipe.py:



Do you please know how the fitted line is calculated?
EDIT: I already figured this out and added figure with explanation in case anyone was interested



In the quality report, what does the vertical line represent? Is it median read quality or similar metric?

Thank you.

[gconcepcion]

Hello,

I would like to learn few details about the following reports from HGAP run, generated by smrtpipe.py:



Do you please know how the fitted line is calculated?
EDIT: I already figured this out and added figure with explanation in case anyone was interested



In the quality report, what does the vertical line represent? Is it median read quality or similar metric?

Thank you.

That's not a vertical line, it's actually the 'same line' as in the first figure that you annotated. It denotes the amount of Mb contained in sequence above a certain read quality. Not sure why the scale on the right side of the figure has been cropped off. It should be the same as the first figure (Mb). I do admit that it looks funny, almost like a vertical line, but not quite. It's always possible there is a bug in the report code, what do your filtered read statistics look like? Pre & Post?

[GenoMax]

@gconcepcion: Consider this a feature request.

Inflexibility (e.g. no way to adjust scales for axes) of plots from SMRTportal analysis reports makes it hard to work with/understand them. Can this be changed in a future version? Is the data used to generate these accessible somewhere in the directory hierarchy?

[gconcepcion]

@gconcepcion: Consider this a feature request.

Inflexibility (e.g. no way to adjust scales for axes) of plots from SMRTportal analysis reports makes it hard to work with/understand them. Can this be changed in a future version? Is the data used to generate these accessible somewhere in the directory hierarchy?

Greater flexibility in terms of charting and reporting options in general is duly noted and certainly on the table for future versions of SMRTAnalysis, but I can guarantee you nothing is going to change in the 2.X.X time frame.

All data used to create the figures can be found in the job directory.
The two particular Filter Report figures posted in this thread are generated by the 'filter_stats.py' script which takes $JOB_DIR/data/filtered_summary.csv as input.

The log for that particular task can be found:
$JOB_DIR/log/P_FilterReports/statsRpt.log

The actual command to generate the figures as well as rest of the filter stats is:
filter_stats.py --output=$JOB_DIR --report=$JOB_DIR/results/filter_reports_filter_stats.json $JOB_DIR/data/filtered_summary.csv


TLDR; take a look at filtered_summary.csv if you want to play with the distributions in your analysis software of choice