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Old 03-03-2017, 07:58 AM   #1
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Location: Houghton, MI

Join Date: Mar 2016
Posts: 8
Default Adding barcode indexes back into FASTQ headers?


I have a set of fastq files from a fungal ITS2 amplicon run on a MiSeq. There are 3 corresponding fastq files: Read1, Read2 and an Index file. In the past, I have worked with fastq files where the Read 1 and Read 2 files (or when they are interleaved into one file) have the barcode indexes at the end of the fastq header lines in the actual Read 1 and Read 2 files; BBMap/BBDuk worked great for processing these files (e.g., adaptor removal, merging reads). However, in my current situation I have the barcodes in their own fastq file, and I can't seem to find a script in BBMap/BBDuk that accommodates my current situation.

My questions are:

Am I missing an argument or script in BBMap that will accommodate my situation?

Or, does anyone know of a function or script outside of BBMap that will take the barcodes indexes in the index file and put them pack into the end of the header lines in the read1 and read2 files? I have found scripts that go the opposite way (e.g., Qiime's script).

Thanks for the assistance
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