Question: Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?
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gravatar for giulia.trauzzi
12 days ago by
giulia.trauzzi0 wrote:

Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have looked into Trimmomatic, Cutadapt (that I have used for the adapter removal) and FLEXBAR. As I have a series of barcodes used throughout my samples (720 samples), FLEXBAR seemed the only one that accepts a .fasta file with the barcodes specified. My question is if I can run the program to detect and remove the barcode sequences across my samples without going through the demultiplexing again. Thanks

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