Hello,
I have what might be a basic question about the file names for importing data into QIIME 2 via the cassava 1.8 importing procedure. These paired-end reads have been demultiplexed via bcl2fastq, processed for low-quality reads and the adapter sequences were trimmed by the sequencing facility already and we received 2 fastq.gz files per sample, which are named like…
SO_7139_5_105_S46_R1_001.fastq.gz
SO_7139_5_105_S46_R2_001.fastq.gz
(Definitions - SO_7139 = project ID, 5_105 = sample ID, S46 = “internal nomenclature”, R1= forward read, R2=reverse read, and 001 = “internal nomenclature”)
Do these need to be renamed similarly to the below (examples from the Cassava 1.8 paired-end data importing tutorial):
e.g., L2S357_15_L001_R1_001.fastq.gz
e.g., L2S357_15_L001_R2_001.fastq.gz
(sampleID_barcode_lanenumber_read_setnumber.fastq.gz)
In that case, is the barcode identifier and lane number arbitrary, as I don’t have this particular info from the sequencing company?
Many thanks from a sequence data novice 