dynast --list option not suitable

[Fra-Mante]

Hello,

I you like to use the dynast pipeline to gerenate the input files for Dynamo. I work with sc-SLAM seq data.
The four supported technologies offerted for dynast aligment are not suitable for my data, because my read1 file started with 10 Barcode bases + 8 UMI bases (inverted compared to scifate). Here an example of a line of my read1 fastq:

TAACTTGGTCGTGAGGGCTTTTTTTT, where TAACTTGGTC is the BC, GTGAGGGC is UMI.
Is it possible to make dynast align suitable for my data structure?

Thanks
Francesca

[Xiaojieqiu]

Hi @Fra-Mante, we are happy to help! unfortunately though dynast's developer @Lioscro has left for industry jobs. I am also starting a new lab soon so my schedule is super busy. I can work on this over the weekends sporadically or after July on full time. However, I can point you to the right direction:

you can figure out adding the support for your experimental system here: https://github.com/aristoteleo/dynast-release/blob/main/dynast/technology.py. Joseph's ngs-tools package should in principle support any UMI/barcode configurations

And then update the align file https://github.com/aristoteleo/dynast-release/blob/main/dynast/align.py correspondingly. I would suggest you to try using chatGPT from openAI or Bard from google to explain the code we wrote for you or even ask them to help you update the code. This may facilitate the whole process.