What are the benefits/disadvantages of allowing multi-hits in tophat ?
Since tophat2.0 the default mapping setting allows for multi-mappers or multi-hits.
Documentation of Tophat 2.0.0
In addition to reporting the best (or primary) alignments (the original TopHat behavior), TopHat 2 can report the secondary alignments up to 20 (the default) paired or single alignments (see --report-secondary-alignments and -g/--max-multihits)
| fastq file | 73485586 | | accepted reads | 86649216 | 118% | | mapped | 77309546 | 105% | | paired | 70973292 | 97% |
Assuming that other downstream programs will see them as independent reads too, especially when the bam is location-sorted, my questions are hence:
- Have you observed artifacts from these multi-mappers ?
- When controlling this with '--max-multihits 1' are the locations picked at random ?
- Or is it best to just ignore them altogether '--max-multihits 0'