Should we report the number of non-trimmed reads?

[henningonsbring]

Is your feature request related to a problem? Please describe. A situation we have ended up in: A sample get too few reads. Then more sequencing data is generated for that sample. After as much as 5 million reads are generated (only 3 million needed) then we have generated as much reads as we have promised. However, more than 2 million reads can be discarded by trimmomatic after trimming leading to that less than 3 million reads are displayed in the QC-report.

Now we have done what we have promised, but it still looks like we have not done that when we deliver to the customer. Should we add a column for total number of non-trimmed reads? Adding such a column would give the customer better understanding for the data.

Describe the solution you'd like

• Total reads should display the raw number of reads
• Add a new column to the report for the number of trimmed reads

Describe alternatives you've considered None

Additional context None

[henningonsbring]

Let's not change this, changing it would cause more confusion since we had things this way for so long. Also we are soon going to run JASEN instead of microsalt and development efforts should be spent there.