multiple primer sets

[a-h-b]

Hi all,

what about incorporating multiple primer set from a multiplex approach (i.e. different genes/regions)?

Activating conda environment: /home/minion/git/dadasnake/conda/cb1403239da0c2b661e2126fd0da49e1 [Tue Dec 14 16:08:35 2021] Error in rule primer_numbers: jobid: 16 output: reporting/primerNumbers_perLibrary.tsv, reporting/primerNumbers_perSample.tsv log: logs/countPrimerReads.log (check log file(s) for error message) conda-env: /home/minion/git/dadasnake/conda/cb1403239da0c2b661e2126fd0da49e1

Originally posted by @thierryjanssens in https://github.com/a-h-b/dadasnake/issues/11#issuecomment-993640170

[a-h-b]

Hi Thierry - can you elaborate on this? what are you trying to achieve, what is your data like, what did you try etc? -A

[thierryjanssens]

I have modified config.test.yaml to include multiple primers (grouped under fwd: and rvs:, taking into account the interdentation):

primers: fwd: sequence: GTGYCAGCMGCCGCGGTAA name: 515F rvs: sequence: GGACTACNVGGGTWTCTAAT name: 806R

Then I have run:

$dadasnake -i ./config/config.test.yaml

$dadasnake -l ./config/config.test.yaml

In which I got the error on the primer number.

The question is if there is any option to use multiple primer sets from a muliplex preparative PCR.

[a-h-b]

can you post the content of logs/countPrimerReads.log ?

currently, we have no option to put several primer pairs into one run. You can of course always run several different config files with different primers and output directories on the same data set. In the first step, dadasnake will select those reads that have the primer pair of your config - so all subsequent steps are independent anyway.

But I suspect you might be after something different? are you hoping to join overlapping amplicons?