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Functional-Genomics / eQTL

eQTL analysis pipeline
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Compute empirical p-values #7

Closed nunofonseca closed 8 years ago

nunofonseca commented 8 years ago

:)

clody23 commented 8 years ago

lot of changes to 4 scripts that need to be integrated into the make files:

1) add aggregate_chromosomes.py to the make file. It generates only 1 hdf5 file with all the SNPs across all the chr analysed. "eqtl_aggregate.py "

2 ) eqtl_trans.py now takes as first argument only one file (generated by the script in 1) ) for trans analysis.

3) eqtl_summary.py now requires another arguments: alpha (significance level) which is only used by trans analysis. " eqtl_summary.py <chr1.hdf5/all_chr.hdf5> ''

4) eqtl_aggregate.py now accepts a list with just one hdf5 file for trans and requires a new argument: n_perm (number of permutations) "eqtl_aggregate.py "