Hi, everyone, I am posting this question for my friend. He is analyzing his CHIP DNA solid deep sequence data, and find out that near 80% reads can not be mapped to the human genome. We are wondering if this high percentage unmapped reads is normal in CHIP DNA deep sequence or there may be something wrong with his result.
Question: Chip Dna Deep Sequence
5
Yang Yang • 50 wrote:
5
Gue Su Chang • 50 wrote:
Your 20% mapping yield looks like low for normal ChIP experiment, even for human. Several factors can reduce this mapping yield. I am wondering which kind of ChIP was used in your case. That is, which kind of proteins was ChIPed?
4
Zhenhai Zhang • 170 wrote:
Hi there,
We have done numbers of SOLiD sequencing run on yeast samples. Normally there are only 30-40 percent of total tags can be uniquely mapped back to yeast genome.
What I would recommend is do it on solexa. You get much higher quality tags.
cheers,
3
Istvan Albert ♦♦ 79k wrote:
I recall that our first samples that we ran on the Solid sequencer have had bad performance. Not quite an 80% loss but around 40%-60% reads were unmappable (yeast). Some other lab members will hopefully chime in with more details.
Please log in to add an answer.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 652 users visited in the last hour