I have a question using trimmomatic to trim adapters from the RNA-seq reads.
I have to QC the reads using trimmomatic but I wonder how it's done.
For example, the sequencing company gave me that the data they gave me were made by "TruSeq Stranded mRNA LT Sample Prep Kit" and say they used "ATTCCT" index.
If I have such info, how do I have to use trimmomatic with these informations?
It would be very helpful if someone can give some advise or pointers.
Thank you very much!.