From b78239e5e46595a83607294794201137baf4c5c8 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Mon, 24 Aug 2020 20:40:01 -0500 Subject: [PATCH] Update create test data script for count #73 --- test_data/createTestData.sh | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/test_data/createTestData.sh b/test_data/createTestData.sh index 47c73d4..0e49060 100644 --- a/test_data/createTestData.sh +++ b/test_data/createTestData.sh @@ -81,10 +81,14 @@ cp Q-Y5F6_1M.se.sorted.deduped.chrY.bam.bai ./NEW_test_data/bam/small/Q-Y5F6_1M. mkdir -p ./NEW_test_data/counts mkdir -p ./NEW_test_data/counts/small -singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5F6_1M.se.featureCounts -cp Q-Y5F6_1M.se.featureCounts ./NEW_test_data/counts/small/Q-Y5F6_1M.se.featureCounts +ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv +ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv +singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam +singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5F6_1M.se.countData +singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se +cp Q-Y5F6_1M.se.featureCounts ./NEW_test_data/counts/small/Q-Y5F6_1M.se.countData cp Q-Y5F6_1M.se.countTable.csv ./NEW_test_data/counts/small/Q-Y5F6_1M.se.countTable.csv +cp Q-Y5F6_1M.se.countTable.csv ./NEW_test_data/counts/small/Q-Y5F6_1M.se.tpmTable.csv mkdir -p ./NEW_test_data/bw mkdir -p ./NEW_test_data/bw/small -- GitLab