Slice It

Documentation

Introduction

SliceIt is a database of genome wide in silicolibrary of predicted sgRNAs for Crispr/Cas9 screens to understand the impact of RBP binding sites perturbation in human cells.

Usage - Search home page

SliceIt currently has 3 search options.
1. Search by Gene name or ENSEMBL ID: This search will return results for the gene of interest.
2. Search by location on a chromosome: This search is for returning results within the range of interest. This search has 2 fields
    Field 1: This is a textbox where the start and end positions are to be entered in "START|END" format (ex. 100000|200000)
    Field 2: This is a selection menu from which the user can select the chromosome of interest for the coordinates.
3. Search by RNA Binding Proteins: This search is for returning results for the RBP of interest. There are 4 fields
    Field 1 & Field 2: This is a selection menu from which the user can select the RBP or corresponding ENSEMBL ID of interest.
    Specificity: The specificity scores can range from 0-100 and the default/minimum recommended value is set to 50
    Efficiency: The efficiency scores can range from 0-1.3 and the default/minimum recommended value is set to 0.3

Usage - Search result page

SliceIt currently has 2 result views.

1. Genome browser view: This is the default result view and we have integrated IGV genome browser to visualize our data.
    Features:
        a. Default tracks: By default, SliceIt loads 6 tracks
                1. Base genome track (hg38)
                2. GWAS
                3. SNP
                4. Binding site (HepG2 Cellline)
                5. Binding site (K562 Cellline)
                6. Predicted guide RNA
        b. Dynamic binding site track selection: A dynamic list of tracks are loaded (for both HepG2 and K562 celllines) relevant to the user's search query and the user has the option to add these tracks to the other default tracks.
        c. Optional Exon expression track: Exon expression tracks across various tissues are also available as optional tracks.
        d. Add your own track from URL: SliceIt also lets the users to add their own tracks to visualize and compare with our data. User can simply click on "Add custom track from URL" button and add enter the link of the datasets. We currently support BED, BAM, Wig, Bigwig and Bedgraph files.

2. Data View: Through this view, user can view/download raw data.
    There are 4 data tabs loaded under this view:
        a. Guide RNA Predictions
        b. SNP from dbSNP
        c. GWAS SNPs
        d. Cis-exon expression across tissues