From 45127fa0acb55fa409602110e5060ef7d742fd8e Mon Sep 17 00:00:00 2001 From: sepro Date: Wed, 26 Jul 2017 13:27:46 +0200 Subject: [PATCH] updated docs (added command for new helper script) --- docs/helper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/helper.md b/docs/helper.md index 5d854fb..53d5592 100644 --- a/docs/helper.md +++ b/docs/helper.md @@ -37,12 +37,13 @@ Script to remove splice variants from a GFF3 file, the longest one is retained. ## Quality control -### htseq_count_stats.py and tophat_stats.py +### htseq_count_stats.py, hisat2_stats.py and tophat_stats.py These scripts will extract the statistics used to assess the quality of samples. python3 htseq_count_stats.py ./path/to/htseq/files > output.txt python3 tophat_stats.py ./path/to/tophat/output > output.txt + python3 hisat2_stats.py ./path/to/hisat2/output > output.txt ## Plots and Graphs