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-rw-r--r-- | brain.documentation/QUICKSTART.rst | 2 |
1 files changed, 1 insertions, 1 deletions
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. |