From 050d7c31cb93ab5a21354c9fad3ce50d44306832 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Fri, 24 Jul 2020 16:22:06 +0200 Subject: [PATCH] Update Wolf tutorial with the OBITools3 --- Wolf-tutorial-with-the-OBITools3.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Wolf-tutorial-with-the-OBITools3.md b/Wolf-tutorial-with-the-OBITools3.md index cc8f0f4..1b2fa21 100644 --- a/Wolf-tutorial-with-the-OBITools3.md +++ b/Wolf-tutorial-with-the-OBITools3.md @@ -49,6 +49,10 @@ And unzip it: obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads +**Note:** For any command, you can also print the result to standard output using the `-` URI: + + obi alignpairedend -R wolf/reads2 wolf/reads1 - > aligned_reads.fastq + ### 3. Remove unaligned sequence records obi grep -a mode:alignment wolf/aligned_reads wolf/good_sequences @@ -57,7 +61,7 @@ And unzip it: 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. +**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