haowenz/chromap_evaluation

Evaluation scripts for Chromap

chromap_evaluation

Evaluation scripts for Chromap manuscript on different data are in their own folders.

Simulated data

We used the paftools to evaluate the alignment results from Chromap and other aligners.

ChIP-seq

All the ChIP-seq evaluation scripts are in its folder.

Hi-C

All the Hi-C evaluation scripts are in its folder.

scATAC-seq

We used the R command

rds<-readRDS("MAESTRO.rds")
write.table(cbind(rds$ATAC@meta.data, Embeddings(rds$ATAC@reductions$umap)), "new.tsv", sep="\t", quote=FALSE) 

to extract clustering information from MAESTRO.