It seems obvious that *2 and *1 fastq are within a pair-end data.
But what does SRR346373.fastq stands for?
It is much smaller than the other two fastq file(1/20 lines of them).
Anyone knows what does it mean?
Sorry to bring you back to this old thread as I noticed something new in relevance to this thread. In the past, when I used wget and local fastqdump, I usually only get the _1.fastq.gz and _2.fastq.gz. But sometimes also the 3rd file for the single reads. However, in my recent direct use of fastqdump (v2.6.3) from the NCBI server with /fastq-dump with "--split-files --gzip sraID" (no choice as the ftp url is no long available), I got _1.fastq.gz and _3.fastq.gz (instead of _2), which seem to represent the pair-end sequences. In agreement with this, on the sra record, it indicates the barcode is between the two reads. So I guess in this case, the _1 and _3 are for pair-end sequences if "--split-files" is used, and I haven't tried to use "--split-3", perhaps it will produce _1 and _2 and the 3rd . Below are the output of the first read from both _1 and _3.