Hi everyone,
I have some SE small RNA-seq data from which I'd like to trim 3' sequencing adapters. I know of several useful trimming programs, like Trimmomatic, Fastx_clipper, and cutadapt, but don't have a good understanding of how to identify the adapters that need trimming.
For example, I am working with Illumina small RNA-seq like a mentioned. How do I know which adapters to input into these trimming programs?
I received the following adapter from the genomics facility:
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG
Do I only trim the portion following the "nnnnnn," or perhaps an inverse complement of that portion? I'm very confused, and appreciate any help you can offer!
Thanks
I have some SE small RNA-seq data from which I'd like to trim 3' sequencing adapters. I know of several useful trimming programs, like Trimmomatic, Fastx_clipper, and cutadapt, but don't have a good understanding of how to identify the adapters that need trimming.
For example, I am working with Illumina small RNA-seq like a mentioned. How do I know which adapters to input into these trimming programs?
I received the following adapter from the genomics facility:
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG
Do I only trim the portion following the "nnnnnn," or perhaps an inverse complement of that portion? I'm very confused, and appreciate any help you can offer!
Thanks
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