Entering edit mode
2.3 years ago
rheab1230
▴
140
Hello everyone, I want to ask in order to do inverse quantile normalization using the gtex pipeline: https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl
eqtl_prepare_expression.py ${tpm_gct} ${counts_gct} ${annotation_gtf} \
${sample_participant_lookup} ${vcf_chr_list} ${prefix} \
--tpm_threshold 0.1 \
--count_threshold 6 \
--sample_frac_threshold 0.2 \
--normalization_method tmm
Can I follow this pipeline for normalization of gene counts for all the snps and not just eQTL. I am not able to understand at what step it specifically select eqtl for study. Can anyone please explain this part to me. Thank you.
