Interleaved FastQ format

Question

[gayal25016]

Hi,

I am new with the interleaved FastQ format and I had one question about their formatting.

1. In the standard format, is the R1 and R2 always following each others ?

i.e. is it

@XXX/1
ATGC
+
IIII
@XXX/2
ATGC
+
IIII
@YYY/1
ATGC
+
IIII
@YYY/2
ATGC
+
IIII

or in some instance could it be

@XXX/1
ATGC
+
IIII
@YYY/1
ATGC
+
IIII
@XXX/2
ATGC
+
IIII
@YYY/2
ATGC
+
IIII

Thanks a lot

Answer 1

[Mensur Dlakic]

They are always following each other. If that's not the case, either some reads are missing or the format is incorrect.

[gayal25016]

Thanks a lot for the clarification :)