I have a fastq file that seems to be contaminated by some sequences contaminating my reagents during library preparation. If I know the reads that came from reagents and I have them in a fasta format, do you think I can eliminate those reads from my fastq file? I want to remove any reads contaminating my fastq file. How can I work this out? 
By using `bbduk.sh` [from BBMap][1]. Provide the contaminants as a multi-fasta file with `ref=` option. 


  [1]: http://seqanswers.com/forums/showthread.php?t=42776