Hi, Hanqing
It is great to learn the inside of ALLCools by following the manual "Basic Clustering Walk-through" (https://lhqing.github.io/ALLCools/cell_level/basic/intro_basic_clustering.html). I am writing to report that the example dataset, Adult (age P56) male mouse brain hippocampus (HIP) snmC-seq2 data from [[Liu et al., 2021] seems missing.
Here is the snapshot of related page:
https://www.dropbox.com/scl/fi/cj21imkd7zbx4qt6ojyh6/missing-input-data.jpg?rlkey=w9itdp1tuwllg0d0uuf6edcfp&st=lzmdjdnj&dl=0
I understand one can generate this combined mcds file from the supplementary table "41586_2020_3182_MOESM6_ESM.xlsx" from Liu et. al 2021 nature paper with dataset from NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132489). In this way, I do combined mcds files of mouse brain HIP regions (16 mcds files with two replications each) as one single file. The last thing is the metadata table. This is crucial for next step filtering, so please help!
Meijiao
Hi, Hanqing
It is great to learn the inside of ALLCools by following the manual "Basic Clustering Walk-through" (https://lhqing.github.io/ALLCools/cell_level/basic/intro_basic_clustering.html). I am writing to report that the example dataset, Adult (age P56) male mouse brain hippocampus (HIP) snmC-seq2 data from [[Liu et al., 2021] seems missing.
Here is the snapshot of related page:
https://www.dropbox.com/scl/fi/cj21imkd7zbx4qt6ojyh6/missing-input-data.jpg?rlkey=w9itdp1tuwllg0d0uuf6edcfp&st=lzmdjdnj&dl=0
I understand one can generate this combined mcds file from the supplementary table "41586_2020_3182_MOESM6_ESM.xlsx" from Liu et. al 2021 nature paper with dataset from NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132489). In this way, I do combined mcds files of mouse brain HIP regions (16 mcds files with two replications each) as one single file. The last thing is the metadata table. This is crucial for next step filtering, so please help!
Meijiao