From 3ad0668c17e2296a85698ea75b193ef5bfb76f37 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 28 Jul 2021 09:18:53 +0200 Subject: [PATCH 1/2] Update output.md --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index d37b183c9..8a7bdadab 100644 --- a/docs/output.md +++ b/docs/output.md @@ -333,7 +333,7 @@ Ancient DNA samples typically have low endogenous DNA values, as most of the DNA

-The main additional useful information compared to [Samtools](#samtools) is that these plots can inform you how many reads had multiple places on the reference the read could align to. This can occur with low complexity reads or reads derived from e.g. repetitive regions on the genome. If you have large amounts of multi-mapping reads, this can be a warning flag that there is an issue either with the reference genome or library itself (e.g. over-amplification of low-complexity regions or library construction artefacts). You should investigate cases like this more closely before using the data downstream. +The main additional useful information compared to [Samtools](#samtools) is that these plots can inform you how many reads had multiple places on the reference the read could align to. This can occur with low complexity reads or reads derived from e.g. repetitive regions on the genome. If you have large amounts of multi-mapping reads, this can be a warning flag that there is an issue either with the reference genome or library itself (e.g. library construction artefacts). You should investigate cases like this more closely before using the data downstream. ### MALT From 230aed68339423be16356f36c76b1d07738c7270 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 11 Aug 2021 15:34:16 +0200 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 32523330c..9f571933e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#771](https://github.com/nf-core/eager/issues/771) Remove legacy code - Improved output documentation for MultiQC general stats table (thanks to @KathrinNaegele and @esalmela) +- Improved output documentation for BowTie2 (thanks to @isinaltinkaya) ### `Dependencies`