Hello, Thank you in advance for your help! I was given some paired end 16S sequences that were run on miseq that have already been paired and demultiplexed, and so there is only one file for each (no R1, R2). When looking at the different import possibilities, this one seems to be appropriate: Ca…

Hello Ariel, Great question! Because your data has already been joined, you can treat it as single-end data. My suggestion is to use the fastq manifest format format, although many options would work. My manifest file would look like this: sample-id,absolute-filepath,direction sample-1,$PWD/some/…

Hi Colin, Thank you so much for getting back to me! A couple of follow-up questions: [image] colinbrislawn: My manifest file would look like this: sample-id,absolute-filepath,direction sample-1,$PWD/some/filepath/sample1_R1.fastq,forward sample-1,$PWD/some/filepath/sample1_R2.fastq,reverse …

[image] ariel: hat have already been paired In QIIME 2 we call these sequences "Joined." [image] ariel: I specifically want to use dada2, does this mean I cannot proceed forward with the current files I’ve been give, and that I need to obtain the un-joined fastq files? Correct - DADA2…

Hello Ariel, Whoops! I mean to post this: sample-id,absolute-filepath,direction sample-1,$PWD/some/filepath/sample1_joined.fastq,forward sample-1,$PWD/some/filepath/sample2_joined.fastq,forward Based on feedback from Matt, I wonder if we should replace forward with joined, like this sample-1,$PW…

Hi Colin, Luckily I was able to (slowly!) obtain the un-joined files. Thank you! Now I am working on importing them! Unfortunately I am getting an error! An unexpected error has occurred: Forward and reverse reads must be provided exactly one time each for each sample. The following samples had …

By the way, here is the command I used and some of the rest of the extremely long error compressed-demux]$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path manifest.txt --output-path ../paired-end-demux.qza --source-format PairedEndFastqManifestPhred33 Traceback (…

@ariel , This error is popping up because the file-path for both the forward and reverse reads are leading to the exact same file. The same file can't be both forward and reverse. If you got the original unjoined reads you should have 2 files per sample. You just need to make sure those 2 files are…

Hi Mehrbod, Thank you so much for your quick response! I accidentally changed it when I tried to change the name for privacy, but here is what it actually looks like: (names changed less) sample-id,absolute-filepath,direction HMP2_J008_R1,$PWD/HMP2_J008_R1.fastq.gz,forward HMP2_J008_R2,$PWD/HMP…

No problem @ariel ! We've all been there, when you have the least amount of time, the most basic things won't work :stuck_out_tongue: You're almost there, now though your sample-ids are different for the same pair. Have a close look at the example again, the sample-id must be identical while the ab…

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Importing paired end reads that have been both paired and demultiplexed

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