Primer Report

[AnCaTjin]

It would be nice to have some kind of report. If the user checks a list of primers he/she can export a report including information about primers which failed and which passed. I am not sure if this maybe belongs to any other issue....

[GaretJax]

It's an issue by itself. Interesting request.

I think this can be implemented as a button in the primerlist to download all the currently listed primers. What would the format of the report be? What data would it contain? Can you maybe send me a sample of what you would expect?

[AnCaTjin]

Primer Report.pdf

[AnCaTjin]

That is just an example. Finally at the end there could be some conclusion: "No primer has a SNPs with frequency above 1 %" or something similar.

[GaretJax]

:+1:

Would you prefer a PDF or an Excel file (easier to copy/paste/edit)?

[AnCaTjin]

PDF Because it is more difficult to edit ;) That is much better for documentation.

[GaretJax]

1) Could you include the primer sequences in the report as well? Maybe then it is necessary to separate the primer pairs in different lines... 2) Is it possible to include more information about the MAFs? Source (gnomAD, 1000Genomes...?), ethnic group You probably included the highest MAF from all sources and all groups? This would obviously take more space but normally only a group of primers would be reported together. I noticed last week that the filter option is not working. 3) Could there be a link to some website like gnomAD or ensembl instead or do you want the people to have an account? 4) Could you include the information about the SNP position in the primer? This would be important, although I see it could disrupt the whole list...

[GaretJax]

1. Can be done, although some of them will have to be trimmed.
2. Not sure if additional MAF information is useful. E.g., if you have a 2.0 MAF for African/Gnomad, nothing will show you that there is also a 1.9 MAF for European on 1000Genomes.
3. What would the link link to? There is no primer information on gnomAD, just the variants, and there can be more than one per primer. The idea is, of course, that everybody has an account, but this is more to be able to protect your labs data that anything else. If you find yourself sharing the report electronically with lots of people not having an account, it's possible to have a special primer detail page for "anonymous" users which, for example, does not allow browsing to other primers.
4. This is also an issue, most of the time there is more than one SNP; what would you show in that case?

What might be possible is to have a first overview as we have now, and after the list, have more precise information but only about the primers failing the checks (similar to the hit detail page, with the variant and MAF details), what do you think? This could easily become one or half a page per primer.

[AnCaTjin]

2. I am not sure I understand what you mean. But the information "forward MAF %" displays the most common SNP's MAF in the population with the highest frequency? The problem is that SNPs in some positions are more important, for example: a primer has a SNP in position 15 with 1,1%, and a SNP in position 1 with 1 %, the more important SNP would be the SNP in position 1 but only the other one is reported. But maybe that is to complicated to start with...? I draw a short suggestion:

[AnCaTjin]

I think the other points are all about the same problem: a primer can/probably will contain more than one SNP. I have to run to a meeting, but will come back to this point later.

[AnCaTjin]

Your suggestion seems to be a nice alternative, the idea with the detailed information after the list. The report you created is a useful overview.

[GaretJax]

@AnCaTjin you can now generate your own reports. Only the filtered primers will be included in them (and filtering is now working again ;-) )

[AnCaTjin]

I generated my first report :)