Hello,
I used to use QIIME1 and am new to QIIME2. I wanted to use QIIME2 to process some public 16S datasets from NCBI SRA. When I downloaded the files they were already demultiplexed and named as below:
SRR000001_1.fastq
SRR000001_2.fastq
SRR000002_1.fastq
SRR000002_2.fastq
SRR000003_1.fastq
SRR000003_2.fastq
I wanted to process them through DADA2 deonise and OTU picking steps, but realized that I have to import them to a .qza file first. I read through the tutorial and was unable to find an intuitive way to do this. I tried:
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path raw_reads_paired/ --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
with the error message:
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: ‘.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’
Should I rename my fastq files to this artificial name format and then use this command? Or is there another easier way to do this?
Thanks very much for any help.
Zhang
!