From 67c361de239155f1eba338cd194346640726cac4 Mon Sep 17 00:00:00 2001
From: peguerin <pierre-edouard.guerin@cefe.cnrs.fr>
Date: Fri, 6 Dec 2019 14:03:50 +0100
Subject: [PATCH] adapter truc
---
02_demultiplex/test/test_demultiplex_flexbar.sh | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/02_demultiplex/test/test_demultiplex_flexbar.sh b/02_demultiplex/test/test_demultiplex_flexbar.sh
index 14894ce..156ed83 100644
--- a/02_demultiplex/test/test_demultiplex_flexbar.sh
+++ b/02_demultiplex/test/test_demultiplex_flexbar.sh
@@ -22,9 +22,6 @@ Primer_R=`pwd`"/02_demultiplex/Primer_R.fasta"
$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags -t 02_demultiplex/test/02_flexbar/"$pref" -n 4
-
-
-
######## cimetiere des commandes non fonctionnelles
#$flexbar -r $R1_fastq -p $R2_fastq -b $Tags -b2 $Tags -a $Primer_F -a2 $Primer_R -at 0.1 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4
#$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags_F --barcodes2 $Tags_R -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4
@@ -32,7 +29,16 @@ $flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags -t 02_demultiplex/test/02_fl
#$flexbar -p $R2_fastq --barcodes2 $Tags -t 02_demultiplex/test2/02_flexbar/"$pref" -n 4
## remove adapters
+for pair1 in `ls 02_demultiplex/test/02_flexbar/*_1.fastq` ;
+do
+pair2="${pair1/_1.fastq/_2.fastq}"
+echo $flexbar" -r "$pair1" -p "$pair2" --adapters "$Primer_F" --adapters2 "$Primer_R" -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref
+done
+
$flexbar -r $R1_fastq -p $R2_fastq --adapters $Primer_F --adapters2 $Primer_R -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4
+
+$flexbar -r 02_demultiplex/test/flexbar_singlebarcode/grinder_teleo1_barcode_S1-01_1.fastq -p 02_demultiplex/test/flexbar_singlebarcode/grinder_teleo1_barcode_S1-01_2.fastq -a $Primer_F -a2 $Primer_R
+
## clean
rm 02_demultiplex/test/02_flexbar/*
\ No newline at end of file
--
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