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Old 03-16-2014, 05:17 PM   #5
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Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default Cutadapt and Trimmomatic

Yes I use trimmomatic and it is great. However, I am using cutadapt now as a different tool for cross validation.

1) with Trimmomatic, yes I do have the adpater sequences in a fasta file, and I can see that the raw data when using grep contains the adapter, however after using trimmomatic and grep, the sequences are removed successfully.

2) However, I am not sure if cutadapt takes an input file. the cutadapt --help takes the input as SPECIFIC SEQUENCES, so this implies taht I would have to enter in ALL the sequences I wish to have cut, or ?

has anyone used cut adapt to cut out the universal adapter AND all the TruSeq Adapter Indices?

Thank you so much again for your input.
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