Illumina MiSeq FASTQ files

[kkggc]

When receiving two fastq files from Illuminia, are they always considered paired-end reads?

[mastal]

It depends on what the files/reads are called.

Depending on how many reads you have, you might have more than 1 file for each sample, with each file having about 4 million or so reads.

If the files are from R1 and R2 paired-end reads, then when you look at the header lines for the reads, they should have read identifiers that are the same except one file having 1:N:0 (R1) and the other file 2:N:0 (R2).

[kkggc]

Okay, but if there are two fastq files for the same sample, then it is paired-end reads? I have files now that I know they are paired-end reads and they do have the R1 and R2 in their file name. Just curious if there is ever a case to have two fastq files for one sample, but not paired-end reads.

[GenoMax]

File names are probably not absolutely certain indicators of two files being paired-end reads (unless you were sure that the sequence provider had followed standard protocols, identical sample_ID/barcodes were included in the file names and the only difference in the names was R1 and R2, as Maria stated before).

[kkggc]

That is understandable. However, I know for sure 100% my two fastq files are for the same sample and are paired-end reads. I am just curious if it is ever a possibility to have two fastq files for the same sample, but NOT paired-end reads.

[GenoMax]

Sure. If you ran a sample multiple times on separate MiSeq runs the resulting file names (with standard post-processing protocol) will be identical (down to the R1 and R2 in names if they are paired-end reads).

Sample file names are using sample_ID inherited from the run samplesheet. So a mistake in the samplesheet could even assign the same name to sample files that are from different samples from 2 separate runs.