FASTQ header format, direction or pair number
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If it's TrueSeq, it's probably this reason: Illumina Read Names: /2 Vs. /3
Isn't it the index read? Index read is /2 and /4?
The sequencing order for Illumina is Read 1 --> [Index 1] --> [Index 2] --> Read 2 (Index 1/2 reads are optional).
If the index reads are being captured in separate files (which some applications like QIIME want) then one potentially gets 4 files per sample (for a 2D run) or 3 files (for a 1D run).
Right, so that would mean this is a run barcoded on one side, with index in file 2?
Correct. Sample file also probably says R3 in the file name, which int11ap1 can confirm.