@@ -89,8 +89,8 @@ The detialed information about these barcode can be found in [SHARE-seq manuscri
# Pipeline output
After successfully running the pipeline, data for each project will be kept in the folder with the same name as the project.
Several QC plots will be generated.\
For ATAC, the most important files are the fragment file after removing duplicates and mito reads (.rmdup.cutoff.bed.gz) and a summarize report (.counts.csv.gz).\
For RNA, the most important files are UMIxCell matrix (.UMIcounts.csv.gz) and a summarize report (.counts.csv.gz).\
For ATAC, the most important files are the fragment file after removing duplicates, mito reads and shifting Tn5 cutting position (.fragments.tsv.gz) and a summarize report (.counts.csv.gz).\
For RNA, the most important files are UMIxCell matrix (.gene.bc.matrices.h5) and a summarize report (.counts.csv.gz).\
This pipeline currently keeps many intermedia files. If preferred, they can be manually removed afterwards.
