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Old 05-22-2017, 03:38 PM   #3
LJC
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Location: Australia

Join Date: May 2017
Posts: 4
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Thanks for your reply Felix.

You're right, it is standard Illumina RNAseq. When i run the default Trimming, as you suggest, my FastQC Adapter plot flatlines, which is great. However, i then get overrepresented sequences that match to specific Index adapters. So i'm not entirely sure what to do. That is why i thought i should specify all of Illumina's Index adapters to trim. I did actually manage to work out how to do this with a fasta file, i also included the 'universal' sequence in the fasta file. After trimming, my FastQC plots showed me that there were no more overrepresented sequences, however then my Adapter plot rose at the end to show that there is still some 'Universal adapter' contamination. I cant seem to figure out how to get rid of the 'universal' adapter contamination and the overrepresented sequences that match to index adapters, all at the same time!

Do you think i can Trim twice? First to get rid of the universal adapter contamination and then again specifying all of the Index Adapter sequences?

Thanks!
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