Help extracting pairwise alignments from MAFs


I’ve been attempting to extract the pairwise alignments from the human and zebrafish genomes using the “Extract Pairwise MAF Blocks” tool but had no success. A few years ago I was able complete this with hg19 and danRer5 and after reading another support ticket from Feb 2019 I assume hg19 is the assembly still indexed. Whenever I run the tool I am met with the error “The MAF source specified (PAIRWISE_hg19_danRer5) appears to be invalid”. I have attempted this with other assemblies and been met with the same error (eg human vs chimp and human vs mouse). Is there something I’m missing?


Hi @jamesdgalbraith,
it seems to be a bug in the tool. The error has been reported Error with Extract Pairwise MAF Blocks tool · Issue #3514 · galaxyproject/tools-iuc · GitHub.


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