Hi, Last year I used QIIME 1 with 4 fastq files (Read1, Read2, Index1, Index2) for my PE Multiplexed MiSeq Data. It took many steps but with your support back then it worked. With QIIME 2, I am not sure where to start because this option / sequencing file option is not listed in the import docs. B…

Hi Matthew, Thank you very much for your help with this. I could re-attached the barcodes to my reads with the merge barcode python script I used with QIIME 1 - but these are still dual barcoded, paired-ended reads that have not been joined. I assume from your statement that cutadapt will not handl…

Hi @Sara_Jeanne08 - I kinda figured you had DI data, but thought "just in case...". [image] Sara_Jeanne08: I assume from your statement that cutadapt will not handle paired-end - dual barcoded reads, since they will need to be joined? Is that correct - QIIME2 doesn’t join reads? Are you talk…

Hi @Sara_Jeanne08 , [image] Sara_Jeanne08: Also, I normally remove chimeras from this seq.fna file but should I wait to import into QIIME 2 before I do this step? Or should I remove chimera’s with QIIME 1 and import the filtered seq.fna file into QIIME 2. QIIME2 supports chimera checking as p…

Hi Matthew, Thank you very much for your help with this. To clarify what I meant by "joining" - My first step is to re-attach my barcodes - then to run the extract barcode script to make a properly formatted barcode file for QIIME 1 (my reads no longer have the barcodes attached after this step). …

Hi @Sara_Jeanne08 , [image] Sara_Jeanne08: As part of demultiplexing with split libraries - I include a quality filter, so I am guessing not being able to use DADA2 may ok for my samples. The quality filtering applied by dada2 is more effective at removing errors than qiime1-style quality fil…

Thank you so much Nicholas. I am glad that with my sequences I can use the quality filtering via deblur. I can not run MacQIIME on my updated Mac but I am working on installing (I found that others have had this issue due to Apple's new security measures). I am glad I can use both QIIME 1 and 2 with…

[image] Sara_Jeanne08: I am a little confused how deblur replaces OTU-Picking Deblur uses a static error profile to resolve "true" sequence variants and identify errors, so is similar to dada2 in that respect (vis-a-vis OTU picking). You can read the original article for more details on how i…

Thanks so much! Your explanation is very helpful!

Hi Nicolas and Matthew, I am trying to use QIIME 2 to work with my now QIIME 1 imported seq.fna files. From what I understand my next step is to quality filter via qiime quality-filter q-score script and then to run deblur denoise-16S. However, I read in the deblur plugin page the following: Usa…

Hi @Sara_Jeanne08 , [image] Sara_Jeanne08: From what I understand my next step is to quality filter via qiime quality-filter q-score script and then to run deblur denoise-16S. My understanding was that you have already demultiplexed these with QIIME1's split_libraries_fastq.py, which already …

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Importing and Demultiplex process for 4 Fastq Files: R1, R2, Index1 and Index2

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