diff --git a/02_demultiplex/test/test_demultiplex_flexbar.sh b/02_demultiplex/test/test_demultiplex_flexbar.sh index 87c4812a71c18d3627d300d6780cd4bc30018494..6858bf0bc2bacf665b4e520974bcdb560b3b0dbc 100644 --- a/02_demultiplex/test/test_demultiplex_flexbar.sh +++ b/02_demultiplex/test/test_demultiplex_flexbar.sh @@ -10,11 +10,23 @@ R2_fastq="${DATA_PATH}"/"$pref"/"$pref"_R2.fastq ## path to 'tags.fasta' Tags=`pwd`"/02_demultiplex/Tags.fasta" -$flexbar -r $R1_fastq -p $R2_fastq --barcodes2 $Tags -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4 +Tags_F=`pwd`"/02_demultiplex/Tags_F.fasta" +Tags_R=`pwd`"/02_demultiplex/Tags_R.fasta" +Primer_F=`pwd`"/02_demultiplex/Primer_F.fasta" +Primer_R=`pwd`"/02_demultiplex/Primer_R.fasta" + +## flexbar - flexible barcode and adapter removal -$flexbar -r $R1_fastq --barcodes $Tags -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" +########## cette commande marche... +$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags -t 02_demultiplex/test/02_flexbar/"$pref" -n 4 + +######## non +$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags_F --barcodes2 $Tags_R -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4 +$flexbar -r $R1_fastq -p $R2_fastq --barcodes2 $Tags -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4 +## remove adapters +$flexbar -r $R1_fastq -p $R2_fastq --adapters $Primer_F --adapters2 $Primer_R -bt 0 -t 02_demultiplex/test/02_flexbar/"$pref" -n 4 ## clean rm 02_demultiplex/test/02_flexbar/* \ No newline at end of file