qiime cutadapt demux failed to exclude reads with fake barcodes in the middle – Technical Support

Below is my command.
qiime cutadapt demux-paired –i-seqs asap2_out/imported/fqMuBiPe-1.qza –m-forward-barcodes-file input//fqMuBiPe-1/metadata.tsv –m-forward-barcodes-column barcode-sequence –o-per-sample-sequences asap2_out/demultiplexed/fqMuBiPe-1-demux.qza –o-untrimmed-sequences asap2_out/demultiplexed/fqMuBiPe-1-untrimmed.qza

The output has many partial reads because there were reads (e.g. reverse complementary, or contaminants) with no barcode at the beginning, but with a fake barcode (randomly matched) in the middle, and qiime mistook it as a barcode and trimmed it and assign it to a sample.

I temporarily use the parameter –p-minimum-length 225 to compromise it, but a better way should be making qiime to limit the location of barcodes to the first n (e.g. 10) bases. Any ideas?


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