Hi! We have recently done the first run on a new NextSeq 500 machine which produced reads with weird FastQC results (attaching below).
This is a paired end sequencing of MNase-seq sample. Libraries were prepared using NEBNext Ultra kit using TruseqLT Illumina adapters. Sequencing was done using NextSeq 500 sequencing kit v2 high output.
I don't have a lot of experience with sequencing so far but FastQC results like these look worrying for me.
Could please anyone explain to me what are these numerous k-mers overrepresented along the reads, including the center of the read (which means that is it is unlikely to be untrimmed adapters)? Is this a problem with library prep or with the actual sequencing on the machine?
This is a paired end sequencing of MNase-seq sample. Libraries were prepared using NEBNext Ultra kit using TruseqLT Illumina adapters. Sequencing was done using NextSeq 500 sequencing kit v2 high output.
I don't have a lot of experience with sequencing so far but FastQC results like these look worrying for me.
Could please anyone explain to me what are these numerous k-mers overrepresented along the reads, including the center of the read (which means that is it is unlikely to be untrimmed adapters)? Is this a problem with library prep or with the actual sequencing on the machine?
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