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Interleaved FastQ format

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

format fastq
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updated by Mensur Dlakic Mensur Dlakic • written by gayal25016 • gayal25016

1 answer

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

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Thanks a lot for the clarification :)

• 0 views • link
written by gayal25016 • gayal25016

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