duplicate reads in enriched samples

[ngs_agd]

Hi all,
I have some RNAseq data (enriched and non-enriched) generated on Illumina. I am seeing a lot of duplicate reads (as well as much higher read depth) in the enriched dataset. Does enrichment result in excess duplicate reads? If yes, what is the best way to deal with them.

Thanks in advance for your help.



P.S. I have been reading SEQanswers for a while now. It is an excellent source of information.

[Seq84]

Hi all,
I have some RNAseq data (enriched and non-enriched) generated on Illumina. I am seeing a lot of duplicate reads (as well as much higher read depth) in the enriched dataset. Does enrichment result in excess duplicate reads? If yes, what is the best way to deal with them.

Thanks in advance for your help.



P.S. I have been reading SEQanswers for a while now. It is an excellent source of information.

I'm interesting in this issue too, in our target resequencing experiment we detected a wide range of % in duplicates (from 2 to 80 %). Is it normal that in a target reseq experiment % of duplicates raise?

[Heisman]

I said in another thread that I communicated by email with an Agilent rep and the main determining factor to duplicates is the number of PCR cycles pre-hybridization. With 7 or 8 cycles I see < 5% duplicates.

[Seq84]

Thanks for your reply Heisman, next time will decrease number of cycles!