Hello,
I'm fairly new to analyzing sequencing data like this. I've noticed this pattern appear several times (both when I look at full runs, or individual samples within a single run).
Sequencer: Illumina NextSeq
Kit: 71 x 10 x 10
I've processed untrimmed reads (though I've also tried trimming, and the same overall pattern appears). At ~38bp, I see a favoring(?) of "A" over "C", "G", or "T". This favoring continues, more-or-less, throughout the remainder of the read.
I'm not quite sure what to make of this pattern. Whenever I run FASTQC on my data, this metric shows up as a "WARN" or "FAIL" every time. I'm not sure what this might be due to. The material we are attempting to use is DNA (from lysate, plant material); not sure if that has an impact or not. Thanks in advance for any advice you all might have!
I'm fairly new to analyzing sequencing data like this. I've noticed this pattern appear several times (both when I look at full runs, or individual samples within a single run).
Sequencer: Illumina NextSeq
Kit: 71 x 10 x 10
I've processed untrimmed reads (though I've also tried trimming, and the same overall pattern appears). At ~38bp, I see a favoring(?) of "A" over "C", "G", or "T". This favoring continues, more-or-less, throughout the remainder of the read.
I'm not quite sure what to make of this pattern. Whenever I run FASTQC on my data, this metric shows up as a "WARN" or "FAIL" every time. I'm not sure what this might be due to. The material we are attempting to use is DNA (from lysate, plant material); not sure if that has an impact or not. Thanks in advance for any advice you all might have!
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