diff --git a/02_demultiplex/test/02_flexbar_adapter/.gitkeep b/02_demultiplex/test/02_flexbar_adapter/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/02_demultiplex/test/test_demultiplex_flexbar.sh b/02_demultiplex/test/test_demultiplex_flexbar.sh index 14894ce4a8d8376fcbedd24bca22e2b5ef0ec0fc..a31946a81fd150acf601b4fd4c74c30a03cdcb7d 100644 --- a/02_demultiplex/test/test_demultiplex_flexbar.sh +++ b/02_demultiplex/test/test_demultiplex_flexbar.sh @@ -19,10 +19,7 @@ Primer_R=`pwd`"/02_demultiplex/Primer_R.fasta" ## demultiplexing -$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags -t 02_demultiplex/test/02_flexbar/"$pref" -n 4 - - - +$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags -t 02_demultiplex/test/02_flexbar_adapter/"$pref" -n 4 ######## cimetiere des commandes non fonctionnelles @@ -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