Problem with MAF (Multiple Alignment Format) files

[dbur...@gmail.com]

Hi,

I'm using IGV_2.8.2 and I'm having problems to visualize all MAF (Multiple Alignment Format) files I tried so far. I started with MAF files related to my own assemblies and didn't work, although I'm able to display any other kind of files (BAM, GFF, BedGraph...). In fact, I'm not even able to see MAF files directly downloaded from UCSC (for example, hgdownload.soe.ucsc.edu/goldenPath/hg19/vsPanTro6/hg19.panTro6.synNet.maf.gz into human genome hg19). The file is loaded but the alignment is empty.

Are there any particular specifications that the MAF format requires to be displayed in IGV browser? Is there any other file format available to visualize "genome-to-genome" alignments?

Thank you,

Demian   

[Jim Robinson]

Hi,

First I should say this is not a focus of IGV,  there are probably better tools for viewing genome-genome alignment.    Having said that,  did you gunzip the maf file and let IGV create an index?   The documentation isn't clear on that.   Creating the index will take some time on first loading.   Your screenshot is too small for me to read but here's what I see from the file you reference

[James Robinson]

Second try on the screenshot

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[Demian Burguera]

Hi Jim,

Yes, it was as simple as gunzip the file in this particular case, thanks! My original problem was related to MAF outputs from LAST web service, but running the program locally solved the issue somehow. I know that IGV is not the optimal tool to visualize genomic alignments, but I need to do it within the context of a genome browser with many other tracks and I am not aware of better tools for that...  

Best,

Demian 

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[James Robinson]

OK great.  I'm not up to date on tools either, the other alternative would be the UCSC genome browser.    Glad it's working for you.   

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