Trimming adapters with custom scoring
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4.8 years ago
aka001 ▴ 190

I was wondering if there is any packages that would allow custom scoring trimming the adapters inside FASTQ files? For example, one can customise minimum alignment score given few base pairs of adapter sequence as well as the scores of matches, mismatches, gap opening, etc.

I have looked several commonly used packages, like trimmomatic, cutadapt, skewer and some others, but seems like none of them has that feature (at least not explained in the manual).

sequence alignment fastq reads adapter • 1.1k views
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If you don't mind, could you explain why you need a custom scoring scheme? What's the particular problem you're trying to overcome?

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I saw several papers mentioning their custom scoring on their method section and I would like to know to what extent this would affect the downstream results compared to the more common ways of trimming.

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I would like to know to what extent this would affect the downstream results

To the extent of number of bases are being selectively let through or removed. If custom scoring is changing the total number of reads drastically then it will affect the results for sure.

If you look at bbduk from BBMap suite there are many parameters you can experiment with.

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To the extent of number of bases are being selectively let through or removed. If custom scoring is changing the total number of reads drastically then it will affect the results for sure.

I couldn't agree more on this, that's why I wanted to see.

Thanks for pointing at bbduk, it is indeed useful and has many options, but after checking it I don't think it has the options that I want. Or did I miss something?

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I did not mean to say bbduk has ability to use custom scoring but it does have multiple options that can allow you to test a range of different options.

If you know programming then it may be possible to change these values (or modify the code) yourself since most of these packages are open source.

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