Find right adapter sequence for trimming
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2.5 years ago
iamsmor • 0

Hello everyone

I am new to RNA-seq analysis. I am trying to clean single end reads data according to fastqc result. It resulted like in example as SRR309133

Overrepresented sequences

Adapter Content

I tried Illumina Adapter Sequences find it there. But after trimming result of fastq doesn't change.How I can find right adapter sequences?

fastqc flexbar RNA-seq • 1.4k views
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You can find Illumina adapter sequences in this PDF. If above graph represents post-trimming results then I would not worry about the residual adapters that remains (unless you are planning to do some de novo work). It looks like flexbar is not very efficient at removing all traces of adapter. fastp, bbduk are better/faster trimming programs.

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Thank you.

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No This graph is represent pre-trimming.This RNAseq was performed in 2009 and I couldnt find which kit was used. I only know it was performed by Illumina genom analyzer IIx.Btw post-trimimming results was same too.So I thought ı couldnot choose right adapter. So problem is how ı can find other way?

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This is just standard Illumina universal adapter. You can find the sequence in the PDF above. See if this works AGATCGGAAGAG (ref: Trimming TruSeq Universal Adapter (Trimmomatic) )

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thank you. Results was better with this sequence. Trimmed all adapter contaminant .

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