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RNA-DNA binding site in Alu Repeat: Why you should allow multiple mapping positions
In a recent publication a RNA binding site was found in an Alu repeat. The signal was lost, when turning off the multiple mapping parameter of the mapping algorithm.
Thus, we recommend to allow multiple mappings, when analyzing ChIPseq data. You might find fancy stuff!
Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, et al. (2013) Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks. PLoS Genet 9(7): e1003588. doi:10.1371/journal.pgen.1003588
Thus, we recommend to allow multiple mappings, when analyzing ChIPseq data. You might find fancy stuff!
Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, et al. (2013) Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks. PLoS Genet 9(7): e1003588. doi:10.1371/journal.pgen.1003588