Would this file be categorized as casava-18-paired-end-demultiplexed format if it starts with this:
@M02825:29:000000000-AT791:1:1101:21434:2058 1:N:0:22
There are 2 files (forward and reverse) and no barcode file.
Would this file be categorized as casava-18-paired-end-demultiplexed format if it starts with this:
@M02825:29:000000000-AT791:1:1101:21434:2058 1:N:0:22
There are 2 files (forward and reverse) and no barcode file.
Hi @ninaxhua.
Are there 2 files per sample or 2 files in total that have all the samples within them? If the former, then I would say yes. If there are only 2 files in total for all of your samples then the reads are not demultiplexed and you would have to use a different importing format.
The first line which you are displaying just hold some information about the run itself.
See here for more detailed description of what that line shows.
There are 2 files per sample, so then it would be casava-18-paired-end-demultiplexed formatted?
It would be if individual sample file names match the formatting described here as per the casva1.8 format. Otherwise I believe you might use paired end Phred format variant to import.
The file name doesn’t match the format. It’s just “samplename_R1.fastq.gz” and “samplename_R2.fastq.gz”. How can we determine if the format variant was 33 or 64?
No problem. Once you’ve created your manifest file as per the linked tutorial earlier, try this:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path pe-33-manifest.csv \
--output-path paired-end-demux.qza\
--source-format PairedEndFastqManifestPhred33
The Phred33 vs Phred64 variant can be a bit tricky to figure out but most current Illumina machines use the 33 variant so if I had to guess I would start there. You can also ask your sequencing facility and they should have this information as well.
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