Gro-seq data

[sikidiri]

Hello,
I have non-unique tags in Gro-seq data. Should I remove redundant tags and work with the unique tags?
Please suggest.

[kerhard]

This depends on what you are planning to do with the data. If you are interested in comparing read counts between two libraries, you can't say much about non-unique reads with respect to a distinct location of the genome. Those reads could have been generated by any of the hundreds or thousands of locations where the repeated sequence resides in the genome.

Maybe someone knows of a more statistically clever way of calculating the probability that a "non-unique" read from a GRO-seq library (i.e., run-on transcription-based, not standard RNA-seq libraries) comes from any one unique location in the genome, but I do not.