A FASTQC report shows an overrepresented sequence defined as "Truseq adapter"
it aligns with high confidence to, say, coronavirus genes
And also why the nucleotide sequence reported by FastQC as "truseq adapter 18" doesn't match it's namesake in one listed in Illumina's official document??????
I am asking this because i wanted to BLAST the overrepresented sequences in my data and see if they come from the ribosomal RNA contamination or not. And with results like THAT even for the adapter sequences I clearly don't understand something
•
written
by
e.r.zakiev •
1 answer
The sequence you provide is the beginning of the Illumina adapter as in the document you link. I see no problem here. It is only 0.27% of reads, so why bother?
As for this BLAST search, I would first of all check that the genome assembly has no leftovers of adapter sequences. But again, it is way less than 1% of sequences, just ignore and continue with analysis.
Log in to answer this question.
-
Low quality of NGS SNP analysis panel
written by kate-nelis •
-
How to interpret that overrepresented and duplicate sequences influence %GC content?
written by tvibhaps •
-
How to find the adapter sequence of an RNAseq dataset?
written by Maryam •
-
Adapter removal using cutadapt and multiqc report:
written by ayeraselvan •
-
How to do preprocessing from fastqc
written by Lulu •
-
Per base sequence content error in RNAseq analysis
written by ahmad.sajad4541 •
-
RNA-seq QC - adapter content and high duplication
written by Simon •
-
When preprocessing the preprocessed reads, will the quality deteriorate?
written by Hang •
-
trimming a paired end sra
written by biology_inform •
-
Adapter content in FASTQ file
written by shivangi.agarwal800
