Trimming Illumina Seq with TRIMMOMATIC
Hello,
I need to remove a common adapter and the barcode sequences from a bunch of samples (short reads - Illumina).
I was able to remove the common adapter with cutadapt from all of the samples, however I would like to know how to use trimmomatic on single end reads to remove my barcode sequences from my samples too. I need to supply a list of barcodes to the program I am assuming but I have no idea how to do this and I am struggling to find anything online.
Thanks
Giulia
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Are these
inlinebarcodes? Are they supposed to be at a fixed location (e.g. beginning of reads)?You can use
bbduk.shwithliteral=sequene1,sequence2 etc. A guide is available for usage.