Question

ChIP-seq vs. RNA-seq

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7.3 years ago

kk1990 ▴ 10

Hi!

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 • 5.9k views

ADD COMMENT • link updated 7.3 years ago by Ryan Dale 5.0k • written 7.3 years ago by kk1990 ▴ 10

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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 REPLY • link 7.3 years ago by GenoMax 141k

score 4 · Accepted Answer · 2017-01-17

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).