From 47cec832c40ea678e29c08af5892384bf5ec2990 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 7 May 2024 14:17:11 -0500 Subject: [PATCH] docs: Add info about the sample column concatinating group and replicate columns --- docs/usage.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 79f2d223..213e4882 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -50,6 +50,12 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +:::info +The sample column is essentially a concatenation of the group and replicate columns. If all values of sample have the same number of underscores, fields defined by these underscore-separated names may be used in the transcript identification produced by the pipeline, to regain the ability to represent different groupings. + +`GM_0h` and `GM_1h` would be grouped for example but `GM0h` and `GM1h` would go through individual transcript identification +::: + ## Alignment Options By default, the pipeline uses [BWA](https://bio-bwa.sourceforge.net/) (i.e. `--aligner bwa`) to map the raw FastQ reads to the reference genome. Research as to which aligner works best with Nascent Transcript and Transcription Start Site assays is pending.