agdenadel / mfass

Code to run analysis in "A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions"

@author : Kimberly Insigne [email protected]

Feb 19, 2018

Please don't hesistate to email me with any questions.

Here's a basic description of where the data lies and how you can use it in your own work.

To locate the raw read counts per bin:

• There is an Excel file with all of the read counts per bin for each construct.
• The version of the SNV library used in the main paper is located at processed_data/snv/snv_v2_all_alignments.csv
• The data for the SRE library is located under processed_data/sre/dhfr/dhfr_all_alignments.csv and processed_data/sre/smn1/smn1_all_alignments.csv for the two different intron backbones.
• Raw sequencing data is not available at this time due to storage constraints but will be made public upon publication.

To located processed and cleaned data:

• For the SNV library, the Excel file is processed by process_scripts/snv/snv_data_clean.R and produces the file processed_data/snv/snv_data_clean.txt. This is probably the file you will want to work with, it contains the calculated exon inclusion index as well as information integrated from the reference (ref/snv/snv_ref_formatted_converted_original_seq.txt)
• processed_data/snv/snv_simple_list.txt contains a simplified list of the SDVs identified in the ExAC library and contains coordinates, the reference and alternate alleles, and the delta exon inclusion index.