@@ -168,10 +168,14 @@ Note that chrom_end is open-end. This output fragment file can be used as input
downstream analysis tools such as [MAESTRO][MAESTRO], [ArchR][ArchR], [signac][signac]
and etc.
For the output, Chromap provide the function to translate input cell barcode to another barcode space.
User can specify the translation file through the option **--barcode-translate**.
The translation file is a two-column tsv/csv file with the original barcode on the second column and the translated barcode on the first column. This is useful for the case of 10x multiome data, where scATAC-seq and scRNA-seq data uses different sets of barcodes.
This option also supports combinatorial barcoding, such as SHARE-seq. Chromap translates each barcode segment provided in the second column to the ID of the first column and added "-" to concatenate the IDs in the output.
Besides, Chromap can translate input cell barcodes to another set of barcodes.
Users can specify the translation file through the option **--barcode-translate**.
The translation file is a two-column tsv/csv file with the translated barcode on the first column
and the original barcode on the second column. This is useful for 10x Multiome data, where
scATAC-seq and scRNA-seq data use different sets of barcodes. This option also supports
combinatorial barcoding, such as SHARE-seq. Chromap can translate each barcode segment provided
in the second column to the ID in the first column and add "-" to concatenate the IDs in the
