We have received our data from the sequencing company which was sequenced on the nextseq. The samples have been de-multiplexed using bcl convert and barcodes have been removed. Previously we have used Casava for importing our demultiplexed samples but this doesnt work with this data. Has anyone successfully imported data into QIIME from the NextSeq and have a recommended code? We can't seem to find a suitable code in the importing tutorial
Welcome to the forum!
There are no issues with importing NextSeq data. I guess, just file names changed and you encountered some errors.
You can either rename file names to be compatible with the CASAVA format or use manifest format instead.
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