Question: Transcriptome assembly if adaptors are not well removed
0
gravatar for Cacau
4.1 years ago by
Cacau480
Canada
Cacau480 wrote:

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 • 889 views
ADD COMMENTlink modified 4.1 years ago by WouterDeCoster44k • written 4.1 years ago by Cacau480
0
gravatar for WouterDeCoster
4.1 years ago by
Belgium
WouterDeCoster44k wrote:

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.

ADD COMMENTlink written 4.1 years ago by WouterDeCoster44k

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

ADD REPLYlink written 4.1 years ago by Asaf8.0k

Reminds me of this blog post: http://www.opiniomics.org/we-need-to-stop-making-this-simple-fcking-mistake/

ADD REPLYlink written 4.1 years ago by WouterDeCoster44k
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