Open fderop opened 7 months ago
Hello,
Thank you for pointing this question out. Actually both the read and UMI count matrix were generated from TF-seq Tools. After comparing the two, we decided to use the read count matrix for 1.3 because: 1. it correlated well with the UMI count matrix; 2. it kept more cells associated with TF-IDs than the UMI count matrix after filtering out cells with low UMIs/reads. At the step of 1.3, we would prefer more cells for downstream processing. The UMI count matrix was used for calculating TF dose as described in 1.5. We have now added more details to the README file.
Hello,
Thank you for the quick response. I have more questions:
Florian
Hi Florian,
Wangjie
Thank you for the explanation, Wangjie. We are looking closely at the paper because we would like to implement it ourselves :)
Glad to hear that you're interested in implementing scTF-seq! Please feel free to contact us for more details. We'd also be happy to help or discuss for any potential collaborations :D
Definitely, will do.
Hello,
Section 1.3 of the README reads:
I was wondering, why was the read count matrix used, and not the UMI count matrix, to generate the TF-cell mapping matrix?