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shimlab / BLAZE

SingleCell Nanopore sequencing data analysis
GNU General Public License v3.0
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Can I use this pipeline with a different Adapter Sequence? #12

Open ShaowenJ opened 8 months ago

ShaowenJ commented 8 months ago

Dear BLAZE developers,

I was wondering if the BLAZE pipeline can be used with a different single-cell protocol than 10X. If our single-cell protocol has a different Adapter sequence, and we have 2 barcode sequences on both sides of the Adapter, would the pipeline also works?

Thanks, Look forward to your reply!

Sefi196 commented 6 months ago

Hi ShaowenJ, Thanks for your question.

At the moment BLAE is only compatible with 10x workflow. If you provide some more detail re the structure of your read we may be able to help modify the workflow.

All the best

Sefi

ljwharbers commented 4 months ago

Hi, I have a similar request. Is it possible to set a certain barcode length? Or that the BC length is taken from the supplied whitelist?

Cheers, Luuk

youyupei commented 3 months ago

Hi @ljwharbers, as BLAZE was originally designed mainly for the 10X kits, the barcode length was hard coded. I can certainly make it specifiable in the future version. For now, if you do want to modify the default barcode length, the only way I can think of is as follows:

  1. clone the BLAZE GitHub directory (the latest commit on the main branch)
  2. modify line 29 of blaze/config.py: DEFAULT_BC_SIZE = 16
  3. go to the root dir of BLAZE (the one with setup.py) and install the modified version by pip install .