From bdf8cfe4a988706bdade8742d05526974947cc72 Mon Sep 17 00:00:00 2001 From: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com> Date: Wed, 4 Dec 2024 19:13:32 -0800 Subject: [PATCH] Fix broken reference database links --- .../Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md b/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md index cec64577..7f1d7c96 100644 --- a/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md +++ b/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-B.md @@ -38,7 +38,7 @@ Amanda Saravia-Butler (GeneLab Data Processing Lead) - Assay-specific suffixes were added where needed for GeneLab repo ("GLAmpSeq") -- The ITS UNITE reference database used was updated to "UNITE_v2023_July2023.RData", from http://www2.decipher.codes/Classification/TrainingSets/ +- The ITS UNITE reference database used was updated to "UNITE_v2023_July2023.RData", from https://www2.decipher.codes/data/Downloads/TrainingSets/ - Several program versions were updated (all versions listed in [Software used](#software-used) below) --- @@ -103,8 +103,8 @@ Amanda Saravia-Butler (GeneLab Data Processing Lead) |Program used| Database| Relevant Links| |:-----|:-----:|--------:| -|DECIPHER| SILVA SSU r138 | [http://www2.decipher.codes/Classification/TrainingSets/SILVA_SSU_r138_2019.RData](http://www2.decipher.codes/Classification/TrainingSets/)| -|DECIPHER| UNITE v2020 | [http://www2.decipher.codes/Classification/TrainingSets/UNITE_v2020_February2020.RData](http://www2.decipher.codes/Classification/TrainingSets/)| +|DECIPHER| SILVA SSU r138 | [https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2019.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/)| +|DECIPHER| UNITE v2023 | [https://www2.decipher.codes/data/Downloads/TrainingSets/UNITE_v2023_July2023.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/)| --- @@ -443,7 +443,7 @@ dna <- DNAStringSet(getSequences(seqtab.nochim)) Downloading the reference R taxonomy object: ```R -download.file( url=“http://www2.decipher.codes/Classification/TrainingSets/SILVA_SSU_r138_2019.RData”, destfile=“SILVA_SSU_r138_2019.RData”) +download.file( url=“https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2019.RData”, destfile=“SILVA_SSU_r138_2019.RData”) ``` **Parameter Definitions:**