From 5608cbcd13c7fd137b6e7ec8e3adea569fbb1cde Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Thu, 12 Dec 2019 17:25:23 +0100 Subject: [PATCH] Update wolf_tutorial --- wolf_tutorial.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/wolf_tutorial.md b/wolf_tutorial.md index 9d0dcf2..a6a6c73 100644 --- a/wolf_tutorial.md +++ b/wolf_tutorial.md @@ -47,23 +47,23 @@ And unzip it: obi less wolf/reads1 -### 2. Assign each sequence record to the corresponding sample/marker combination - -Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before aligning the paired-end reads: - - obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences -R wolf/reads2 wolf/reads1 wolf/identified_sequences - -### 3. Recover the full sequences from the partial forward and reverse reads +### 2. Recover the full sequences from the partial forward and reverse reads - obi alignpairedend wolf/identified_sequences wolf/aligned_reads - -### 4. Remove unaligned sequence records + obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads + +### 3. Remove unaligned sequence records obi grep -a mode:alignment wolf/aligned_reads wolf/good_sequences +### 4. Assign each sequence record to the corresponding sample/marker combination + + obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences wolf/good_sequences wolf/identified_sequences + +Note: Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before aligning the paired-end reads, BUT it is not recommended to do so for usual data, as ngsfilter will not be able to detect and cut out partially sequenced primers. + ### 5. Dereplicate reads into unique sequences - obi uniq -m sample wolf/good_sequences wolf/dereplicated_sequences + obi uniq -m sample wolf/identified_sequences wolf/dereplicated_sequences ### 6. Denoise the sequence dataset