From 42c944bff9d9483942a65bf7de56e8532df8d938 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Sun, 30 Jun 2019 14:54:54 +0200 Subject: [PATCH] Update wolf_tutorial --- wolf_tutorial.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/wolf_tutorial.md b/wolf_tutorial.md index 2577aab..45be4db 100644 --- a/wolf_tutorial.md +++ b/wolf_tutorial.md @@ -49,15 +49,21 @@ Not working yet... ### 1. Import the sequencing data in a DMS +Download the reads: + +[wolf_F.fastq.gz](/uploads/09dada3587189c3b3a7af7024981c074/wolf_F.fastq.gz) + +[wolf_R.fastq.gz](/uploads/a95dbad14b75474c8307cab56fa083ca/wolf_R.fastq.gz) + 1. Import the first set of reads, with : - obi import --quality-solexa wolf_tutorial/wolf_F.fastq wolf/reads1 + obi import --quality-solexa wolf_tutorial/wolf_F.fastq.gz wolf/reads1 `--quality-solexa` is the appropriate fastq quality option because it's an old dataset, `wolf_tutorial/wolf_F.fastq` is the path to the file to import, `wolf` is the path to the DMS that will be automatically created, and `reads1` is the name of the view into which the file will be imported. 2. Import the second set of reads: - obi import --quality-solexa wolf_tutorial/wolf_R.fastq wolf/reads2 + obi import --quality-solexa wolf_tutorial/wolf_R.fastq.gz wolf/reads2 3. Import the [ngsfilter file](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) describing the primers and tags used for each sample: