I found the belowfew software to remove adapters:
- TagDust - eliminate artifactual sequence from NGS data http://www.biomedcentral.com/1471-2164/12/382 http://bioinformatics.oxfordjournals.org/content/25/21/2839.full
- FAR: http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php? title=Main_Page
- Trimmomatic: http://www.usadellab.org/cms/index.php?page=trimmomatic
Adapters the same like PCR fragments?
Running one of the software above would it gives me the same results like MarkDuplicates.jar?
Thank you in advance.