Splint and adapter sequences : B-Cell dataset

[mbosio85]

Hello, I am trying to replicate the results from your paper for the 96 single-cell part as I would like to get acquainted with the tool and see all results.

I am trying to get all the needed information to urn C3POa to work but:

• I cannot find the DNA splint sequence (is the one in #3 ok for these samples ? )
  • and I don't know how to retrieve this -a sequence of cDNA adapter sequences in fasta format. Sequence names must be 3Prime_adapter and 5Prime_adapter

Could you share the required fasta with the 96 adapter sequences and the Splint one if it's different?

thanks a lot, Mattia

[rvolden]

The splint sequence is fine, but I'm adding splint.fasta with the exact sequence that was used in the paper. I'm also adding adapter.fasta that contains the 3' and 5' adapters used in post processing. I can supply you with a demultiplexing script if you need one. How are you multiplexing your samples?

[mbosio85]

Hi, Thanks a lot for your answer. If I get it right I will process the ONT data from the 96 samples of B-cells using the splint and adapter you provide. This will generate an output with reads from 96 samples in one single output that will need to be demultiplexed. If you already have a script for those 96 sample I would like to give it a try.

About your question, I don't have my own samples yet, I wanted to try the tool and replicate your results from the paper so I can see the kind of data it outputs (I am actually interested seeing what happens in the percentage of genes with coverage but no isoform detected by Mandalorion II ). Once I am acquainted with the software and data analysis I'll proceed thinking more about the experimental design details.

thanks again! Mattia

[rvolden]

Sorry this took a while to get to you, but I've added the indexes and the demultiplexing script to the paper directory on the repo. Let me know if you have any other questions and I'll get back to you faster than last time