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hello there! thanks for making all the packages and notebooks.
I was looking at the mtSNVs in one of the rds files downloaded from here https://doi.org/10.6084/m9.figshare.23290004 and trying to do the same filtering as described in the nature paper. However after my filtering there are ~ 43k mismatches left, a number much higher than what you stated in the paper (~3 or 4k mt mutations). Could you please point me to the actual code or maybe a more specific description about how you processed the mutation calls? thank you very much!
The text was updated successfully, but these errors were encountered:
Dear @chilampoon
Thank you for your question and your interest.
In the redeemR package the function Create_redeemR and Vfilter_v4 are the two major function together doing the filtering. The source code are in the folder of R/BuildTree.R Perhaps you can check if you have filtered by maxctscut=2 which is to only take variants that have at least 2 or more than 2 molecules per cell in at least one cell. This is a filtering to remove potential NUMT influence. But please check the source code as well.
Please feel free to let me know if you have any other questions.
hello there! thanks for making all the packages and notebooks.
I was looking at the mtSNVs in one of the rds files downloaded from here https://doi.org/10.6084/m9.figshare.23290004 and trying to do the same filtering as described in the nature paper. However after my filtering there are ~ 43k mismatches left, a number much higher than what you stated in the paper (~3 or 4k mt mutations). Could you please point me to the actual code or maybe a more specific description about how you processed the mutation calls? thank you very much!
The text was updated successfully, but these errors were encountered: