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seqan / flexbar

flexible barcode and adapter removal
BSD 3-Clause "New" or "Revised" License
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paired end barcode demultiplexing #27

Open Grelot opened 4 years ago

Grelot commented 4 years ago

I want to perform demultiplexing on paired-end fastq files but with barcodes for each pair fastq file.

This basic command works well

$flexbar -r $R1_fastq --barcodes $Tags

This one too

$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags

But now i want to check specific barcodes on the second pair:

$flexbar -r $R1_fastq -p $R2_fastq --barcodes $Tags_F --barcodes2 $Tags_R

This command gave me the following output:

               ________          __              
              / ____/ /__  _  __/ /_  ____ ______
             / /_  / / _ \| |/ / __ \/ __ `/ ___/
            / __/ / /  __/>  </ /_/ / /_/ / /    
           /_/   /_/\___/_/|_/_.___/\__,_/_/     

Flexbar - flexible barcode and adapter removal, version 2.5

Local time:            Wed Dec  4 14:31:03 2019

Target name:           flexbar
File type:             fastq
Reads file:            /share/reservebenefit/working/Input_data/Outputs/grinder_teleo1/grinder_teleo1_R1.fastq
Reads file 2:          /share/reservebenefit/working/Input_data/Outputs/grinder_teleo1/grinder_teleo1_R2.fastq   (paired run)
Barcode file:          /share/reservebenefit/working/pierre/eDNA--benchmark_pipelines/02_demultiplex/Tags_F.fasta
Barcode file 2:        /share/reservebenefit/working/pierre/eDNA--benchmark_pipelines/02_demultiplex/Tags_R.fasta

threads:               1
max-uncalled:          0
min-read-length:       18

barcode-trim-end:      ANY
barcode-threshold:     1
barcode-match:         1
barcode-mismatch:     -1
barcode-gap:          -9

Barcode:               Sequence:
S1-01                  ^AACAAGCC
S1-02                  ^TGAGAGCT
S1-03                  ^ACAACCGA
S1-04                  ^TTACGCCA
S1-05                  ^GGAGAAGA
S1-06                  ^CAGGCTAA
[...]
S29-11                 ^TCTGTTCG
S29-12                 ^ACCAGTAC

Barcode2:              Sequence:
S1-01                  ^AACAAGCC
S1-02                  ^TGAGAGCT
[...]

S29-10                 ^CTTGTGAC
S29-11                 ^TCTGTTCG
S29-12                 ^ACCAGTAC

Processing reads ...Error opening file: flexbar_barcode_S14-06-S1-02_2.fastq

It also generated empty files with name as combination of tags

flexbar_barcode_S1-01-S1-01_1.fastq
flexbar_barcode_S1-01-S1-01_2.fastq
flexbar_barcode_S1-01-S1-02_1.fastq
flexbar_barcode_S1-01-S1-02_2.fastq
flexbar_barcode_S1-02-S1-01_1.fastq
flexbar_barcode_S1-02-S1-01_2.fastq
flexbar_barcode_S1-02-S1-02_1.fastq
flexbar_barcode_S1-02-S1-02_2.fastq
flexbar_barcode_S1-03-S1-01_1.fastq
flexbar_barcode_S1-03-S1-01_2.fastq
flexbar_barcode_S1-03-S1-02_1.fastq
flexbar_barcode_S1-03-S1-02_2.fastq
flexbar_barcode_S1-04-S1-01_1.fastq
flexbar_barcode_S1-04-S1-01_2.fastq
flexbar_barcode_S1-04-S1-02_1.fastq
flexbar_barcode_S1-04-S1-02_2.fastq
flexbar_barcode_S1-05-S1-01_1.fastq
flexbar_barcode_S1-05-S1-01_2.fastq
flexbar_barcode_S1-05-S1-02_1.fastq
flexbar_barcode_S1-05-S1-02_2.fastq
flexbar_barcode_S1-06-S1-01_1.fastq
flexbar_barcode_S1-06-S1-01_2.fastq
flexbar_barcode_S1-06-S1-02_1.fastq
[...]
lcamVz commented 2 years ago

Did you got it to work for pair-end?