Issue Viewing Peaks based on Loaded C. elegans Genome

[SM Pyonteck]

Good afternoon,

I hope this email finds you well. I am getting in touch because I am having some issues viewing my wig files based on different versions of the C. elegans genome that I load into IGV. 

I am using version IGV_2.3.68 on a Macbook air.

The wig file was actually generated based on ChIP-seq data alignment to the WBcel235 (equivalent to WS241 / WS245 annotation) genome build. When I load my wig file (link included) using the downloaded genome C. elegans (WS220) the data looks great and I see nice peaks. I have taken screenshots specifically at region: V:10,458,373-10,485,782, data range: 1-2000. However, the WS220 annotation was based on an older C. elegans genome build, so I would like to view the data in a more updated version. Whenever I load the exact same wig file into IGV using the downloaded genome C. elegans (ws241) or C. elegans (WS245), I can see all of the reference genes but no peaks whatsoever using the exact same data range and regions (screenshots attached). Can you please help me figure out why I can't view my peaks in these more updated genome versions? Thank you so much for your help.

All the best,

Stephanie 

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 HIF-1_OR3350_WA_L4_IP_GoatV-aGFP_Rep1.tagAlign_...

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[Jim Robinson]

This is usually caused by name sequence name mismatches between the wig and fasta (genome) files.  Can you verify that the chromosome names match?  If not you can either rename them in the fasta, or the wig.  Its also possible to create an alias file if renaming isn't possible.

Be careful about viewing data aligned to one genome in another.  If only annotations have changed that is fine, but if the fasta file has changed the peaks will be mis-aligned.

Jim

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[SM Pyonteck]

Great! Thank you so much for getting back to me, Jim! I will look into the chromosome naming issue and keep my fingers crossed that it resolves it. Much appreciated!

All the best,

Stephanie