Too many RefSeqs! Help please

[BPenn]

I mostly use IGV to remap mutations that don't use my reference transcripts. My process typically involves loading hg19, entering the chromosomal location of the mutation that came in on a non-preferred transcript, and looking at the amino acid numbering in my preferred transcript. 

My understanding is that IGV just loads whatever RefSeqs it finds in NCBI. The problem is that some genes like BRCA1 recently jumped from a few transcripts to over 300 (see BRCA1 for example). Finding my preferred transcript in IGV is like finding a needle in a haystack. I just have to scroll down and hover over hundreds of transcripts to find mine.

I have tried setting the Feature Label Field to "id" to display the NM IDs instead of the gene name under each transcript in IGV, but it is still pretty much useless.

Is there a way to sort the RefSeq alphabetically and/or search for a particular RefSeq in the IGV viewer?

Thanks!

[igv-help]

Yes there are a lot of BRCA1 transcripts.

For hg38 I would suggest you use the "MANE" annotation track, but this doesn't exist for hg19.   I suggest you try the "Refseq Select" track from UCSC, which I think is a lift-over of the MANE transcripts.   This should have a single transcript per gene.   You can load it from "File > Load from URL",   paste in the following URL:

https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeqSelect.txt.gz

[BPenn]

Fantastic! This workaround is going to save me a lot time. I sometime use Hg38. How do I display the MANE annotation track?

[igv-help]

For hg38 its under "File > Load from Server > Annotations > Genes".

[Bodvael]

Wow! I wish I had known about this before. Thank you so much!

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