Use the FASTX-Toolkit to trim out the barcodes from the FASTQs by position, then quality filter them.
1 | trim_and_filter(fastq, temp_dir, quality_cutoff, bc_start, bc_end)
|
fastq |
path to a fastq file |
temp_dir |
a character string giving the path to a directory to use for temporary intermediate files |
quality_cutoff |
an integer indicating the quality cutoff to be used |
bc_start |
an integer indicating the position in the read where the barcode starts |
bc_end |
an integer indicating the position in the read where the barcode ends |
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