From 82fba7d65d7d5e3436c7b4b53b77c430ab553d65 Mon Sep 17 00:00:00 2001 From: "Zhang, Dabao" Date: Fri, 20 May 2022 13:48:49 -0400 Subject: [PATCH] Update gexp_prep_gtex.sh --- script/gexp_prep/gexp_prep_gtex.sh | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/script/gexp_prep/gexp_prep_gtex.sh b/script/gexp_prep/gexp_prep_gtex.sh index 636db32..621354f 100755 --- a/script/gexp_prep/gexp_prep_gtex.sh +++ b/script/gexp_prep/gexp_prep_gtex.sh @@ -7,13 +7,13 @@ cp $SIGNET_TMP_ROOT/tmpg/subjid_wb_common.txt subjid_wb_common.txt awk '{print $2}' $reads | tail -n+4 > GTEx_genename -echo -e "Looking for the samples for $tissue tissue \n" +echo -e "Looking for the samples for $tissue tissue... \n" Rscript $SIGNET_SCRIPT_ROOT/gexp_prep/gexp_prep_gtex.R "reads='$reads'" "tpm='$tpm'" "tissue='$tissue'" "anno='$anno'" && tabix -l $SIGNET_TMP_ROOT/tmpg/GTEx_snp.vcf.gz > vcf_chr_list -echo -e "Begin normalizing \n" +echo -e "Normalizing gene expressions...\n" python3 $SIGNET_SCRIPT_ROOT/gexp_prep/eqtl_prepare_expression_igt2log.py $tpm \ $reads \ @@ -25,5 +25,4 @@ python3 $SIGNET_SCRIPT_ROOT/gexp_prep/eqtl_prepare_expression_igt2log.py $tpm \ --sample_id_list sample_ids_tissue.txt -echo -e "Normalizing finished \n" - +echo -e "Normalizing gene expressions... Completed!\n"