Hi Everyone,
I'm new to the forum and have a question regarding an odd pattern in a new transcriptome dataset of Illumina HiSeq 2000 (v1.9) paired end 100bp reads.
Looking at the FastQC outputs provided with the raw data from our sequencing provider, I noticed that across 10 TrueSeq mRNA libraries (2 tissue types, different sexes, replicate individual fish), all 2nd pair reads appear to start with the same two bases - either an 'AT' or 'TT' or 'GA'. Base quality is good overall. See attached FastQC graphs as an example of 'AT' bias. The 1st pair reads do not show this bias.
I have emailed my sequencing provider for clarification, but I also wanted to know if anyone here has come across this pattern? Any thought on what the cause might be?
I'm new to the forum and have a question regarding an odd pattern in a new transcriptome dataset of Illumina HiSeq 2000 (v1.9) paired end 100bp reads.
Looking at the FastQC outputs provided with the raw data from our sequencing provider, I noticed that across 10 TrueSeq mRNA libraries (2 tissue types, different sexes, replicate individual fish), all 2nd pair reads appear to start with the same two bases - either an 'AT' or 'TT' or 'GA'. Base quality is good overall. See attached FastQC graphs as an example of 'AT' bias. The 1st pair reads do not show this bias.
I have emailed my sequencing provider for clarification, but I also wanted to know if anyone here has come across this pattern? Any thought on what the cause might be?
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