diff --git a/README.md b/README.md index d7f3676..41000a3 100644 --- a/README.md +++ b/README.md @@ -58,23 +58,23 @@ bean-count-samples \ ### Input file format #### 1. gRNA_library.csv -File should contain following columns. Also see examples for [variant library](crispr-bean/tests/data/test_guide_info.csv) and [tiling library](crispr-bean/tests/data/test_guide_info_tiling.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) variant screen design * `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.