Hello,

I am working on NGS data generated by Illumina Hiseq 2000 and using CASAVA
to convert .bcl file to fastq. As CASAVA replaces all adaptor sequences to
N, I have ended up with a doubt. I find a lot of reads with N in between
the read. I am assuming that may be adaptors and casava has replaced those
adaptor sequences to N. But I am not sure about it. Hence can somebody give
me some suggestions on this? This type of masking is also creating problem
in trimming such N's in the terminals, as I am not sure whether it is
adaptor or actual sequence. I request your help.

Example is given here,

@HWI-ST846:39:C00DDACXX:8:1101:10834:2386 1:N:0:
TAATGAGGATCTCATACAGACTCAACAAAAGGCGAAGAAANNNNNNNNNNNNAGGAGGTGTGGGCTGCACCACTGCTTTTCAAAAGGAACTCCATTGTTGA
+
@@@DDDD8CDFFFIIE?FH?FGGDAFFIE;@CFED)??FG############--;?CA;6?BBCCB@BBBB
?<:(:ABBB:A:@4?<?BBBBBBBEABB?@

Regards,
mlsc

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