FASTQ header format, direction or pair number
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7.8 years ago
int11ap1 ▴ 480

I have the following headers:

Pair 1: @NS500352:99:HMFTGBGXY:1:11101:14196:1038 1:N:0:ATCACG

Pair 2: @NS500352:99:HMFTGBGXY:1:11101:14196:1038 3:N:0:ATCACG

Why pair 2 has a value of 3 in the read number field? Shouldn't it be 2?

fastq • 4.1k views
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If it's TrueSeq, it's probably this reason: Illumina Read Names: /2 Vs. /3

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Isn't it the index read? Index read is /2 and /4?

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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).

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Right, so that would mean this is a run barcoded on one side, with index in file 2?

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Correct. Sample file also probably says R3 in the file name, which int11ap1 can confirm.

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