diff --git a/.test/3-prime-config/config/config.yaml b/.test/3-prime-config/config/config.yaml index b69d19de..f4ff4fa3 100644 --- a/.test/3-prime-config/config/config.yaml +++ b/.test/3-prime-config/config/config.yaml @@ -123,7 +123,7 @@ params: # This setup is for Lexogen QuantSeq FWD data, based on (but simplfied): # https://faqs.lexogen.com/faq/what-is-the-adapter-sequence-i-need-to-use-for-t-1 # For more details, see the QuantSeq section in the `config/README.md` file. - adapters: "-a r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=7;max_error_rate=0.005" + adapters: "-a 'r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=7;max_error_rate=0.005'" extra: "--minimum-length 33 --nextseq-trim=20 --poly-a" # reasoning behind parameters: # For reads that are produced by 3’-end sequencing, depending on the protocol, it might be recommended to remove some leading bases (e.g. see https://www.nature.com/articles/s41598-019-55434-x#Sec10) diff --git a/config/README.md b/config/README.md index fe3932e9..bc994104 100644 --- a/config/README.md +++ b/config/README.md @@ -56,7 +56,7 @@ For Lexogen 3' QuantSeq data analysis, please set `experiment: 3-prime-rna-seq: For more information information on Lexogen QuantSeq 3' sequencing, see: https://www.lexogen.com/quantseq-3mrna-sequencing/ In addition, for Lexogen 3' FWD QuantSeq data, we recommend setting the `params: cutadapt-se:` with: ``` - adapters: "-a r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=7;max_error_rate=0.005" + adapters: "-a 'r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=7;max_error_rate=0.005'" extra: "--minimum-length 33 --nextseq-trim=20 --poly-a" ``` This is an adaptation of the [Lexogen read preprocessing recommendations for 3' FWD QuantSeq data](https://faqs.lexogen.com/faq/what-is-the-adapter-sequence-i-need-to-use-for-t-1).