If the RAM is not more than 4 Gb, what problems does the annotate run with and what information does it lose?
And what is the difference between its output and normal?
If you are using -noann it will skip the Genomic Annotation part completely. Check the How Basic Annotation Works segment to know the details.
Do you mean that you only need to work with ram4 Gb and above?
Otherwise there is no point in working with homer?
Depends upon the annotations you are looking for, if the genomic annotation is crucial then definitely -noann will be pointless. You can also utilize the UseGalaxy platform to do the analysis.
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