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Transcriptome assembly if adaptors are not well removed

I am wondering how the removal of adaptor sequences will impact the transcriptome assembly. For example, in 10% of my reads contain adaptors which are not removed. If I try to assemble the transcriptome, will some of my unigene dataset contain adaptors? Besides, will the result be different if I use a genome-guided or de novo asssembly method?

rna-seq assembly
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updated by WouterDeCoster WouterDeCoster • written by Cacau Cacau

1 answer

I think assembly is one of the things were you definitely want to remove adapters, if not you'll have spurious overlaps creating erroneous contigs/transcripts, just because they share an adapter.

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written by WouterDeCoster WouterDeCoster

I've experienced such a catastrophic event. On the other hand you might get cool chimeric proteins.

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written by Asaf Asaf

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