dedicated to assays, protocols, and information from the EuroClonality-NGS Working Group - also refer to https://euroclonalityngs.org/
If you're interested in processing data from EuroClonality-NGS SOPs for marker identification and clonality assessment [http://www.euroclonality.org/protocols/],
after you log in with a suitable account, switch to 'EC-NGS' user modes (top-left corner).
number of cells in sample
- This number should be the number of patient cells you used, which is then used as the denominator for normalisation (marker cells / patient cells).
- This number has nothing to do with EC-NGS spike-ins, those are dealt with automatically, incl. the tool using them to convert marker reads to cells for normalisation.
- You can provide this information in 'processing', either through a small widget or through a samplesheet and a column “cells” - post-processing, you can still provide it in 'file' through a samplesheet or in 'questions' through a small widget we have. Otherwise, we cannot use the spike-ins to normalise abundances - if all is OK, click on the 'use' widget to see the normalised abundances.
EuroClonality-NGS primer sets
- There are currently eight (8) EuroClonality-NGS primer sets: IGH-VJ (in fact, IGH-VJ-FR1 to 3), IGH-DJ, IGK-VJ-Kde, intron-Kde, TRB-VJ, TRB-DJ, TRD, TRG
- The primer set names on the sample names are auto-detected, but they need to be around underscores or provided through a samplesheet
- otherwise we think the sample is 'pooled' and we report on all possible primer sets used in the analysis.
Doesn't necessarily affect the analysis itself, but makes for a healthier and helpful output (e.g. less alarms).