I know that there are several approaches to detect contamination in submitted NCBI transcriptome studies databases, but since I am doing a literature review, I would appreciate if you add up to my list with your suggestions.
Srinivas M Srikanth
Hi Bilgenur,
Do you mean vector sequences?, you can use the NCBI Univec database sequences and match with the RNA-Seq data to eliminate any contaminating sequences. Follow this link for more information:
https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/
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Deepika Srivastava
VECSCREEN only screens the vector sequences not removes them so you have to write a script to remove it (I used it personally). You can use SeqClean tool it will remove all the vectors then input its .cln and .qual file into "cln2qual". I think it will work for you. :)
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