Question: ChIP-seq vs. RNA-seq
gravatar for kk1990
3.5 years ago by
kk199010 wrote:


I have two sets of data in fastq format, say A and B. How can I tell which one comes from ChIP-seq and which from RNA-seq experiment? Do you know any tricky way to find out?

rna-seq chip-seq ngs • 4.0k views
ADD COMMENTlink modified 3.5 years ago by Ryan Dale4.9k • written 3.5 years ago by kk199010

A similar question was recently asked: Characteristic features of Chip-seq and RNA-seq data

Take a look at the answers there. This sort of thing should not be happening in the first place. In case this is a test of some sort then we should not be helping you anyway :)

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax85k
gravatar for Ryan Dale
3.5 years ago by
Ryan Dale4.9k
Bethesda, MD
Ryan Dale4.9k wrote:

Map them both to a reference; the RNA-seq library will be more likely to have splice junctions (look for "N" in the BAM cigar string) and will be sparse in intergenic regions, while the ChIP-seq will have more even coverage, less dynamic range, and will probably have some low-level signal in most places. If it's a decent ChIP experiment, you'll see clear punctate peaks (if it's from transcription factors) or broad domains (from e.g., histone modification ChIP).

ADD COMMENTlink written 3.5 years ago by Ryan Dale4.9k
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