ChIP seq basic terminology: what is a ChIP-seq tag?

Question

[Mohit]

Hello ,

Greetings!!!

Can I know the meaning of the ChIP-seq tags?

[GouthamAtla]

https://en.wikipedia.org/wiki/ChIP-sequencing

http://www.nature.com/nrg/journal/v10/n10/abs/nrg2641.html

Answer 1

[Istvan Albert]

Tag is what chipseq people call sequencing reads - it is a somewhat arbitrary and obtuse word that typically is never defined properly.

I am guessing that the reason for the new terminology is that they are trying to say that their methods don't really care about the actual alignment of the reads (for example variations relative to the genome). Chip-seq methods typically only account for the 5' end coordinate of the alignment of the read in the genome, hence the results are mostly reduced to counts at given coordinates.

[Dataman]

Does tag in other contexts refer to the number of molecules that are sequenced in one experiment?

tag count, which is the number of different DNA molecules that can be sequenced and mapped to the reference genome.

(source: https://doi.org/10.1016/j.cell.2011.01.003)

[Istvan Albert]

alas, the definition given in that paper is fundamentally wrong - which irks me more than usual because the first author took my course in Bioinformatics and is using software that I wrote to analyze the data ... I can pretty much guarantee you that my software is not counting DNA molecules :-/

What they call DNA molecule is in reality a DNA fragment (obviously a very different concept). One molecule may produce varying numbers of fragments, hence the uncertainty to how to interpret the results of a ChIP sea method.

Tag counts usually are a synonym to "mapped reads"