From 6640b06b7d3d994ba12815aef22da9f315c4225b Mon Sep 17 00:00:00 2001 From: Lan Hui Date: Wed, 23 Apr 2025 18:50:08 +0800 Subject: Useful sed command for getting the number of columns in TPM.txt --- brain.documentation/QUICKSTART.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'brain.documentation') diff --git a/brain.documentation/QUICKSTART.rst b/brain.documentation/QUICKSTART.rst index 271cd4d..eb75c61 100644 --- a/brain.documentation/QUICKSTART.rst +++ b/brain.documentation/QUICKSTART.rst @@ -326,7 +326,7 @@ A2_S1_quant.txt is generated by Salmon (see download_and_map.py), and has the fo .. make_parameter_rnaseq.py assembles all small TPM files. Specify on the top a gene list in parameter_for_buildRmatrix.txt so that only the TPM values for these genes are collected. -- Output: a matrix of TPM values, stored in the file TPM.txt (under *Data/history/expr*). If a gene has isoforms, then use the largest TPM value from these isoforms. +- Output: a matrix of TPM values, stored in the file TPM.txt (under *Data/history/expr*). If a gene has isoforms, then use the largest TPM value from these isoforms. You can get the number of columns in TPM.txt using sed Linux command: awk -F'\t' '{print NF; exit}' Data/history/expr/TPM.txt Getting a final TPM matrix involves first downloading RNA-seq data and mapping them. -- cgit v1.2.1