Merge branch 'dev' of https://github.com/pinellolab/crispr-bean into dev

README.md

@@ -58,23 +58,24 @@ bean-count-samples \
 
 ### Input file format
 #### 1. gRNA_library.csv
-File should contain following columns. Also see [example](crispr-bean/tests/test_guide_info.csv).
+File should contain following columns. 
 * `name`: gRNA ID column
 * `sequence`: gRNA sequence
 * `barcode`: R2 barcode to help match reporter to gRNA
 * 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 (gRNAs are designed to target specific variants and ignores bystander edits)
+* For variant library (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` : 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)
+* For tiling library (gRNAs tile coding / noncoding sequences)
   * `strand`: Specifies gRNA strand information relative to the reference genome.
   * `chrom`: Chromosome of gRNA targeted locus.
   * `start_pos`: gRNA starting position in the genome. Required when you provide `strand` column. Should specify the smaller coordinate value among start and end position regardless of gRNA strandedness.
 
+Also see examples for [variant library](tests/data/test_guide_info.csv) and [tiling library](tests/data/test_guide_info_tiling.csv).
 
 #### 2. sample_list.csv
 File should contain following columns with header.