Beginner level trimming question

[all_your_base]

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

[all_your_base]

If anyone has any insight for me, please share! I am eager to trim with confidence

[swbarnes2]

That whole thing is likely the adaptor, with the nnnnnnn being the index, so that will be different for every sample. That sample might be in the fastq name, otherwise, ask whoever prepped the library.

[JackieBadger]

Depending on how small you sequences are, you will see some/all/no adapter.
If your sequences are all the same length you can usually eye ball adapters at the end and do some simple batch trimming in for example Galaxy...but there are programs that check to see if adapters are present. PRINSEQ or FASTQC can do this.
I think also the EMBOSS (maybe tagDUST) will do this to. I think they are also implemented in Galaxy (which is easy to use)

[all_your_base]

Thanks for the help everyone.

@swbarnes2, you were indeed correct, the whole thing was the adapter. I was able to find the adapter, including the multiplexing tags, in its entirety for many reads. I tried several different adapter clipping programs but settled on trimmomatic. It's multithreading capability was great.

Thanks for the help!