# does q2-cutadapt support dual indexed reads?

**URL:** https://forum.qiime2.org/t/does-q2-cutadapt-support-dual-indexed-reads/11708
**Category:** User Support
**Created:** [September 28, 2019, 12:36am UTC](https://forum.qiime2.org/t/does-q2-cutadapt-support-dual-indexed-reads/11708 "2019-09-28T00:36:49Z")
**Posts on this page:** 1
**Showing post:** 5

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### Author: ![LuSanto](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/l/49beb7/32.png) [@LuSanto](https://forum.qiime2.org/u/LuSanto)
#### Post date: [October 1, 2019, 6:16pm UTC](https://forum.qiime2.org/t/does-q2-cutadapt-support-dual-indexed-reads/11708/5 "2019-10-01T18:16:48Z")

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Thanks. These are the final commands for importing and demultiplexing, and both run with no errors.

qiime tools import --type MultiplexedPairedEndBarcodeInSequence --input-path raw-data --output-path raw-data.qza

qiime cutadapt demux-paired --i-seqs raw-data.qza --m-forward-barcodes-file metadata.tsv --m-forward-barcodes-column BarcodeSequenceForward --m-reverse-barcodes-file metadata.tsv --m-reverse-barcodes-column BarcodeSequenceReverse --o-per-sample-sequences cutadapt-demux.qza --o-untrimmed-sequences unmatched-barcodes.qza

**However, I run into a new problem.** Sequences are only being demultiplexed based on the F barcode. Furthermore, as the F barcodes are repeated, they are only used for demultiplexing the first time they appear in the metadata file. I’m attaching a part of metadata.tsv and the manifest obtained after demultiplexing. Could the problem be the repeated F barcodes? Why aren't the R primers being used? I tried inputing R barcodes in either 5'-3' or 3'-5' orientation. [MANIFEST.txt](https://forum.qiime2.org/uploads/short-url/p8uD0xrP0Ke6PG9fi1jz4yJrmOk.txt) (585 Bytes) [metadata.tsv](https://forum.qiime2.org/uploads/short-url/rjuVKjW3UsKphZCg3TIVAxsGv4H.tsv) (713 Bytes)

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