From 1e7852b2879ae39d3ce73cee16e5b83ae27df085 Mon Sep 17 00:00:00 2001 From: Adam Stuckert Date: Tue, 9 Apr 2019 18:18:55 -0400 Subject: [PATCH] clarify trimming/cleaning --- quant-README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/quant-README.md b/quant-README.md index bec5c20..eb3ea28 100644 --- a/quant-README.md +++ b/quant-README.md @@ -1,6 +1,6 @@ # General usage for quant.mk -This make file is meant to be used to trim adaptors, error correct reads, and pseudo-map to a reference transcriptome (for example one produced by the Oyster River Protocol...) for an individul sample. The user specifies some sample information, then the make file runs through to quantification of that sample. +This make file is meant to be used to pseudo-map to a reference transcriptome (for example one produced by the Oyster River Protocol...) for an individul sample. This script does not trim adaptors or clean reads, as we have found that this does not improve performance and massively increases mapping time for each sample. The user specifies some sample information, then the make file runs through to quantification of that sample. # Usage: First, the user needs to activate the relevant conda environment using `source activate orp_v2`