Do you know what the sequences are? If so, the tool "NGS: QC and manipulation -> Clip adapter sequences" is a good choice.
If you do not know what these are, try contacting whomever did the sequencing. Or you can try using "FastQC" to identify them.
Best, Jen, Galaxy team
I used FASTQC and from its results checked the overrepresented sequences and used Clip. Now, the problem i am facing is i have a reference genome but its annnotation file is in asn format, how can i use this in galaxy.
Also, please advise in customizing the parameter for Tophat2 likle how to calculate inner mean distance etc