Dear Qiime2 users, I am newbie to bioinformatic analysis and for qiime2 as well. We are using Ion torrent PGM platform for V4 16SrRNA region. After sequencing, output are all .fastq files (according to our samples) and one nomatch.fastq, kindly see the attachment ( [nomatch_fastq] . It seems our seq…

Hi @khemlalnirmalkar I have imported in QIIME2 my fastq files from PGM using the next command line: qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path manifest_file.csv --output-path demux.qza --source-format SingleEndFastqManifestPhred33 You have the instructions t…

Hello Colin, Thanks for your reply. I checked the "fastq manifest format" and as I understood this command is not gonaa work with my datas. Yes, I have one fastq file per sample please see the attachment fastq.png" [fastq] " but I don't have forward and reverse sequences separately. Each fastq data…

Good morning Khemala, Thanks for posting your files for me. I think this format will work for importing: Single End Fastq Manifest Phred33 . This format only needs a forward sequences, which is a perfect fit for your data. So when the tutorial says reverse, you just don't include those lines. [i…

Hello Colin, Good Morning, Thanks for your useful comments. I am sorry, I didn't explain properly in my previous post. Here in attachment " [Figura%201] " explains the outline of Ion Torrent PGM platform. So we get the merged FASTQ files from forward and reverse reads. In previous post's image " [fa…

Good morning Khemlal, That's a very helpful diagram! I'm not very familiar with the Ion Torrent PFM platform, but here is what I would try first. Build your manifest file and save it as se-33-manifest.csv. Maybe like this: sample-id,absolute-filepath,direction # Lines starting with '#' are ignor…

Thanks for that @colinbrislawn ! We probably want to import as type SampleData[JoinedSequencesWithQuality], instead: qiime tools import \ --type 'SampleData[JoinedSequencesWithQuality]' \ --input-path se-33-manifest.csv \ --output-path single-end-demux.qza \ --source-format SingleEndFastqManife…

I am working with demultiplexed data from PGM Ion Torrent, like khemlalnirmalkar user, and I think that I understood how to import the data through the manifest file.csv (until my understanding a file with a list of all your fastq files paths. In your example all reads are in forward in the column …

The "direction" doesn't necessarily matter in that manifest, so long as it is all one, or all the other (forward or reverse) when importing single-end reads. Since you have demultiplexed reads, go ahead and import them as single-end, then trim the barcodes using q2-cutadapt . You might need to set up…

Thanks for your comments @thermokarst @colinbrislawn @MMC_northS . In the second figure from my previous post, files from V3-341F8 to V3-341F46.fastq are containing both forward and reverse sequences. I am sorry but I am bit confused. Since i don't have barcodes.fastq. file and I am worrying how t…

Hi @khemlalnirmalkar - If your reads are already demultiplexed, there is no need to worry about barcodes (just make sure they have been removed from your demultiplexed reads). Please see my post above about importing these demultiplexed reads. Since these reads are already technically "joined", y…

Hello Qiime2 users @Nicholas_Bokulich @thermokarst @colinbrislawn @MMC_northS As per your suggestions, again tried to import my .fna files (demultiflexed) using qiime tools import \ --input-path seqs.fna \ --output-path seqs.qza \ --type SampleData[Sequences] for the next step but I could n…

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