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halelab / GBS-SNP-CROP

GBS SNP Calling Reference Optional Pipeline
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Step3.Demultiplexing_message_all_Done_but_empty_fastq_outputs #8

Closed el42008 closed 8 years ago

el42008 commented 8 years ago

Hi,

I am trying to demultiplex my samples using the 3 script. I provided the barcode ID files as asked and teh seed_name of my PE_R1 and R2parsed.fastq files obtained with script2. The scripts works fine as checked in the error file, and gives me the message DONE Please, see the 'demultiplexed' directory But all I get is all the files of the genotypes but empty. So it does the ./multiplexed directory and produces all the 48 files taht correspond with the genotypes but the end up empty.

Thank you very much

arthurmelobio commented 8 years ago

Hi,

Please, check a coulpe of things:

  1. Blank spaces in your barcode ID file.
  2. The barcode sequence attached in the end of each read header.
  3. If you are using the correct -d flag for your data type.

Please, use the google group for the next questions ...

Thanks, Arthur.

el42008 commented 8 years ago

Thanks,

I have checked all and I have another question I posted in google group. Thanks very much for asking so quick