The tracy decompose process yields mutation data which are ultimately saved as csv files. Note, that one entry in a mutation table is a single mutation, i.e. multiple mutations for a single sample collected in a single Indigo visualisation file can appear in the table. To be able to link mutation data entries to respective Sanger trace electropherograms), links to Indigo visualisations in the filesystem need to be provided.
In addition, this link should direct the user automatically to the mutation position of interest in the electropherogram (which is usually manually done by clicking respective buttons within the Indigo visualization table). Currently, the mutation position is not highlighted but this could be done by a simple vertical line.
Two options were discusssed.
Option 1
Add links to Indigo visualisation directly as a column to mutation tables from post-processing steps of the tracy decompose output (.csv files). The advantage is here that the user can navigate the table my mutation detection/no mutation detection and select the rows with relevant visualisation to look at.
A potential disadvantage is that this table would be displayed in the vuegen report with links which would not direct the user to the corresponding files when clicked. We would have to make a note that only copying links is possible followed by opening in the Bulk URL Opener (see below).
Option 2
Add links to a completely separate file where the user has to select relevant files to be opened using the Bulk URL Opener (see below). This might be a simpler approach compared to option 1. However, it requires the user to navigate two separate tables (mutation and visualisations).
Bulk URL Opener
For inspecting multiple Sanger traces using this approach, the Bulk URL Opener, which is a GoogleChrome extension, can be used (as suggested by @Skitionek) : https://chromewebstore.google.com/detail/bulk-url-opener-tab-manag/nipkhjpemhflobkeegjpflbfmplpndje
The
tracy decomposeprocess yields mutation data which are ultimately saved as csv files. Note, that one entry in a mutation table is a single mutation, i.e. multiple mutations for a single sample collected in a singleIndigovisualisation file can appear in the table. To be able to link mutation data entries to respective Sanger trace electropherograms), links toIndigovisualisations in the filesystem need to be provided.In addition, this link should direct the user automatically to the mutation position of interest in the electropherogram (which is usually manually done by clicking respective buttons within the Indigo visualization table). Currently, the mutation position is not highlighted but this could be done by a simple vertical line.
Two options were discusssed.
Option 1
Add links to
Indigovisualisation directly as a column to mutation tables from post-processing steps of thetracy decomposeoutput (.csvfiles). The advantage is here that the user can navigate the table my mutation detection/no mutation detection and select the rows with relevant visualisation to look at.A potential disadvantage is that this table would be displayed in the vuegen report with links which would not direct the user to the corresponding files when clicked. We would have to make a note that only copying links is possible followed by opening in the
Bulk URL Opener(see below).Option 2
Add links to a completely separate file where the user has to select relevant files to be opened using the
Bulk URL Opener(see below). This might be a simpler approach compared to option 1. However, it requires the user to navigate two separate tables (mutation and visualisations).Bulk URL Opener
For inspecting multiple Sanger traces using this approach, the
Bulk URL Opener, which is a GoogleChrome extension, can be used (as suggested by @Skitionek) : https://chromewebstore.google.com/detail/bulk-url-opener-tab-manag/nipkhjpemhflobkeegjpflbfmplpndje