Update README.md

README.md

@@ -55,11 +55,10 @@ File should contain following columns.
 * In order to use accessibility in the [variant effect quantification](#bean-run-quantify-variant-effects), provide accessibility information in one of two options. (For non-targeting guides, provide NA values (empty cell).)   
   * Option 1: `chr` & `genomic_pos`: Chromosome (ex. `chr19`) and genomic position of guide sequence. You will have to provide the path to the bigwig file with matching reference version in `bean-run`. 
   * Option 2: `accessibility_signal`: ATAC-seq signal value of the target loci of each guide.  
-* For variant screen 
-  * Here, gRNAs are designed to target specific variants and ignores bystander edits.
-
+* For variant screen (gRNAs are designed to target specific variants and ignores bystander edits)
     <img src="imgs/variant_screen_gRNA_design.svg" alt="variant screen design" width="500"/>
-  * `target_col` (default "target"): This column denotes which target variant/element of each gRNA. This is not used in `bean-count[-samples]` but required to run `bean-run` in later steps.
+  * `target` : This column denotes which target variant/element of each gRNA. This is not used in `bean-count[-samples]` but required to run `bean-run` in later steps.
+  * `target_group [Optional]`: If negative/positive control gRNA will be considered in `bean-qc` and/or `bean-run`, specify as "NegCtrl"/"PosCtrl" in this column. 
   * `target_pos [Optional]`: If `--match_target_pos` flag is used, input file needs `target_pos` which specifies 0-based relative position of targeted base within Reporter sequence.
 * For tiling screen (gRNAs tile coding / noncoding sequences)
   * `strand`: Specifies gRNA strand information relative to the reference genome.