Entering edit mode
7.9 years ago
int11ap1
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490
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?
If it's TrueSeq, it's probably this reason: Illumina Read Names: /2 Vs. /3
Isn't it the index read? Index read is /2 and /4?
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).
Right, so that would mean this is a run barcoded on one side, with index in file 2?
Correct. Sample file also probably says R3 in the file name, which int11ap1 can confirm.