average number of duplicated reads for NGS
0
0
Entering edit mode
9 weeks ago
igorm ▴ 20

Hi,

I am looking for some wisdom ngs regarding read duplication.

What is the expected/acceptable number of duplicated reads when sequencing human dna, for example at average coverage 1x? Are there any official statistic on this topic? How to improve the protocol to minimize the duplicated reads?

Thanks.

NGS illumina bwa • 254 views
ADD COMMENT
1
Entering edit mode

expected/acceptable number of duplicated reads when sequencing human dna, for example at average coverage 1x

Don't think there is an expected/acceptable number. One would always want to minimize PCR/technical duplicates. Some of this is going to depend on quality of the libraries. There are going to applications where duplication would be normal/expected (RNAseq etc).

How to improve the protocol to minimize the duplicated reads?

There are PCR-free methods/kits that minimize duplicates. There will likely be optical/clustering duplicates depending on type of sequencer used (Duplicates on Illumina ).

ADD REPLY
0
Entering edit mode

Thanks for fast reply GenoMax and advice. Based on your experience what is the percentage that would clearly seem unexpected? For example 10% duplicates at 1x coverage on PCR library reasonable or not?

ADD REPLY

Login before adding your answer.

Traffic: 3009 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6