olgert denas  committed 77d246b

how bnMapper and pslMap use alignment files

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 This is filtering out all peaks that incurr a gap (insertion in mouse) of more than 9 bases as well as peaks of which less than 70% of bases are mapped.
+=== Note: relation with pslMap ===
+In case you are looking for consistent results between pslMap (utility from UCSC that performs mappings of generic PSL alignments) and bnMapper, you need to be careful at least on the (chain) alignments you choose to use. If your features are short enough and do not overlap with duplications on neither species and if you run pslMap with the //-swapMap// options, you should get the similar results. For example, to map //human// peaks into mouse you need to use the //mm9ToHg19.over.chain// alignment file for both pslMap (with the -swapMap option) and bnMapper. This because bnMapper maps only on the //target-to-query// direction (target and query as defined in the chain file).
+Notice, however, that **bnMapper and pslMap are different**, specially when features overlap with duplications on either species or when they span multiple chains. Thus, you are not guarantied to always get the same results.