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JiekaiLab / scTE

MIT License
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Details about running scTEATAC in 10X format #69

Closed zys-BIG closed 10 months ago

zys-BIG commented 11 months ago

Hello @jphe, thanks for you great work! I am wondering if I can run scTEATAC on 10X cellranger-arc output bam file or I have to modify the raw fastq files from the beginning and then map by bowtie2. The "Analysis of scATAC-seq data" part of the README really make me confused.

zys-BIG commented 11 months ago

And since I have the 10X multiome data, is it reasonable to perform scTE only on the scRNA-seq data for downstream analysis but not scATAC-seq data? Thank you very much!

jphe commented 11 months ago

For cellranger output bam file, you need copy the cell barcode to read name first, you can do this with sinto (https://timoast.github.io/sinto/), and then provide the converted bam file to scTE

zys-BIG commented 10 months ago

For cellranger output bam file, you need copy the cell barcode to read name first, you can do this with sinto (https://timoast.github.io/sinto/), and then provide the converted bam file to scTE

Thank you very much! It works for me.