can we use the same aligner to map reads obtained from ChIP-seq and RNA-seq expriments to the reference genome?

Question

[yingshanwang1999]

Can we use the same aligner to map reads obtained from ChIP-seq and RNA-seq experiments to the reference genome? For example on the different scenarios like i) Can an aligner that was designed to align ChIP-seq data be also used for aligning RNA-seq data? ii) Can an aligner that was designed to align RNA-seq data be also used for aligning ChIP-seq data?

[GenoMax]

You can use an aligner like bbmap which is splice-aware and can also align different types of data. You will need to use appropriate settings when doing the alignments for the two kinds of data. A guide is available to use BBMap.

Answer 1

[Istvan Albert]

In general, it is not recommended to do so (unless you are working with an organism that does not have splicing).

Running aligners is a very simple task (compared to all other tasks) thus there is little reason to use the same aligner.