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Short Insert size and aggressive trimming

Hi All

When I have short insert size where it is possible that the adapters run into the reads. I trimmed the adapters using cutadapt/trimgalore. FastQC reports regarding adapter contents show no adapters. Is this sufficient or I do need to do more aggressive adapter trimming? Keeping in mind that we still have around 70% alignment with Tophat or 75% mapping rate with Salmon. My professor suggest that I still have adapters in the reads. Is it possible if FASTQC report no adapters. So how can I know how much more trimming is yet needed?

Thanks

rna-seq adapter trimming insert size
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written by Sharon Sharon

I was helping someone else with trimming this morning and you may want to try the suggestions there with your data (C: Adapter percentages in the reads )

You will never be able to map 100% of the reads. Best you can do is reach low 90's. At this point you can either move to the next step (using data from TopHat or Salmon) or try a different aligner (STAR or BBMap to see if you get better results). In any case do not expect to get 100% read mapping.

BTW: Many aligners will soft-clip adapters/unmapped sequences so some choose not to trim initial data (I don't).

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written by GenoMax GenoMax

My professor suggest that I still have adapters in the reads.

Just because (s)he feels so? Post FastQC images from before/after if you want to get second opinion here.

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written by GenoMax GenoMax

Thanks Gabriel. Will give it a try :)

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written by Sharon Sharon

let me know if it works and need further help :-)

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written by Gabriel R. Gabriel R.

Sure Gabriel, thanks so much :)

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written by Sharon Sharon

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