Mercurial > repos > iuc > dada2_removebimeradenovo
changeset 10:1770d188f72d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72
| author | iuc |
|---|---|
| date | Sat, 07 Dec 2024 08:47:32 +0000 |
| parents | 073608a50ac3 |
| children | |
| files | dada2_removeBimeraDenovo.xml |
| diffstat | 1 files changed, 4 insertions(+), 1 deletions(-) [+] |
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--- a/dada2_removeBimeraDenovo.xml Fri May 24 11:43:18 2024 +0000 +++ b/dada2_removeBimeraDenovo.xml Sat Dec 07 08:47:32 2024 +0000 @@ -100,7 +100,10 @@ The frequency of chimeric sequences varies substantially from dataset to dataset, and depends on on factors including experimental procedures and sample complexity. Here chimeras make up about 21% of the merged sequence variants, but when we account for the abundances of those variants we see they account for only about 4% of the merged sequence reads. -Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited. In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline. +Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited. +In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline. +You can check for present primer sequences with the tool `dada2: primer check` + @HELP_OVERVIEW@ ]]></help>