I was uploading my RNA-seq assembly in TSA and I am not sure how to proceed. 743 sequences from my assembly got flagged with Code(VECTOR_MATCH) UniVec vector: gnl|uv|NGB00150.1:1-46 Ambion FirstChoice RLM-RACE 3' RACE adapter. I find it weird because I thought I already removed adapters prior to assembly using trimmomatic + fastqc. I have searched for the sequence of the adapter. What I want to know is how do I safely trim out the adapter sequence. I mean what if the vector is at the middle portion of the sequence, is it still acceptable to just remove the chunk and merge the two segments together? I could not find any sources to answer this at the moment that's why I am here.
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