###################################################
######--Macromap sQTL public data repository--#####
###################################################

This directory contains summary statistics and other results from the MacroMap sQTL study (see El Garwany et al. for more details on how different analyses were performed).
#######################################
##########--Directories--##############
######################################
There are for directories, each containing subdirectories with a README.txt file explaining the columns. Where publicly available column documentation is available, we reference the relevant URLs

#########################
1-sqtl_summary_statistics
#########################
Full summary statistics of sQTL split by chromosome (nominal pass;; see https://qtltools.github.io/qtltools/ for more details)

#######
2-coloc
#######
Results of colocalisation of each condition sQTLs with genome-wide significant loci from 22 immune-mediated diseases

##################
3-sqtl_permutation
##################
Permutation summary statistics listing the most significant variant for each gene, along with adjusted empirical P-values and P-values derived from a beta distribution (permutation pass; see https://qtltools.github.io/qtltools/ for more details)

##################
4-phenotype_tables
#################
Contains three types of files:
a) {condition}_perind.counts.txt
contains the counts of split reads as a proportion of total reads in corresponding leafcutter intron cluster (formatted as count_intron/sum_count_cluster; see https://davidaknowles.github.io/leafcutter/index.html for more details)


b) {condition}_perind.counts_normalised.gz
contains filtered and normalised intron usage ratios using the prepare_phenotype_table.py script of leafcutter (see https://davidaknowles.github.io/leafcutter/articles/sQTL.html for more details). Specifically, these are intron usage ratio normalised via rank-based inverse normal transformation (see publication for more details)

c) {condition}_junclist_gencodev45.annot
Intron annoation generated by regtools (generated using regtools annotate; see https://regtools.readthedocs.io/en/latest/commands/junctions-annotate/ for more details on the columns)