5d4ceca3972f7cc98ceb6aee0ec02b4541d52527
lrnassar
Fri Sep 10 11:38:14 2021 -0700
Updating old link to MANE, no RM
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NCBI RefSeq (hg19/hg38): This track collection contains three subtracks that select the
most relevant transcript for all or a subset of genes, with slightly different aims:
- RefSeq Select: NCBI manually selects few, usually one,
transcript per gene called "RefSeq Select", based on a lot of criteria.
The criteria include manual curation, whether a transcript appears in LRG sequences,
whether it is well conserved and many more.
Example use cases are comparative genomics and variant reporting. This subset
is available in the RefSeq Select track under NCBI RefSeq.
- MANE: RefSeq and the EBI
also select one transcript for every protein coding gene that is annotated exactly
the same in both Gencode and RefSeq, a project called "MANE select", which is another subtrack of NCBI RefSeq. "MANE select"
can be considered a subset of RefSeq Select.
- HGMD: For the special case of clinical diagnostics
where an even more reduced number of transcripts simplifies visual inspection,
we provide another subtrack, "RefSeq HGMD". It contains
(usually) a single transcript only for genes known to cause human genetic diseases and
the transcript is the one to which all reported HGMD clinical variants can be mapped to.
This transcript set is also a good choice for variant reporting.
This is rather complicated. Can you tell me which gene transcript track I should use?
For automated analysis, if you are doing NGS analysis and you need to capture
all possible transcripts, GENCODE provides one of the most comprehensive gene sets. For human