Question: Chip Dna Deep Sequence
5
gravatar for Yang Yang
9.4 years ago by
Yang Yang50
Yang Yang50 wrote:

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.

solid chip-seq • 2.6k views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 20 • written 9.4 years ago by Yang Yang50
5
gravatar for Gue Su Chang
9.4 years ago by
Gue Su Chang50
Gue Su Chang50 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?

ADD COMMENTlink written 9.4 years ago by Gue Su Chang50
4
gravatar for Zhenhai Zhang
9.4 years ago by
Zhenhai Zhang170
502 Wartik Lab, Penn State Univ
Zhenhai Zhang170 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,

ADD COMMENTlink written 9.4 years ago by Zhenhai Zhang170
3
gravatar for Istvan Albert
9.4 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
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.

ADD COMMENTlink written 9.4 years ago by Istvan Albert ♦♦ 79k
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