202747ec0531c9c8c6eab66377bd6bc84e1a1b57
lrnassar
Wed Feb 26 11:29:49 2020 -0800
Touching up RefSeq composite page to clarify new RefSeq Select track refs #24787
diff --git src/hg/makeDb/trackDb/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html
index 9446061..11b49da 100644
--- src/hg/makeDb/trackDb/refSeqComposite.html
+++ src/hg/makeDb/trackDb/refSeqComposite.html
@@ -10,31 +10,31 @@
Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions,
submit additions and corrections, or ask for help concerning RefSeq records.
For more information on the different gene tracks, see our Genes FAQ.
Display Conventions and Configuration
This track is a composite track that contains differing data sets.
To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to
hide. Note: Not all subtracts are available on all assemblies.
-The subtracks available for this track include:
+The possible subtracks include:
- RefSeq aligned annotations and UCSC alignment of RefSeq annotations
-
RefSeq All – all curated and predicted annotations provided by
RefSeq.
-
RefSeq Curated – subset of RefSeq All that includes only those
annotations whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for
protein-coding genes on the mitochondrion; YP is used for human only.)
-
RefSeq Predicted – subset of RefSeq All that includes those annotations whose
accessions begin with XM or XR.
-
@@ -42,38 +42,40 @@
do not fit the requirements for inclusion in the RefSeq Curated or the
RefSeq Predicted tracks.
-
RefSeq Alignments – alignments of RefSeq RNAs to the $organism genome provided
by the RefSeq group, following the display conventions for
PSL tracks.
-
RefSeq Diffs – alignment differences between the $organism reference genome(s)
and RefSeq transcripts. (Track not currently available for every assembly.)
-
UCSC RefSeq – annotations generated from UCSC's realignment of RNAs with NM
and NR accessions to the $organism genome. This track was previously known as the "RefSeq
Genes" track.
-
- RefSeq Select+MANE (subset) – Subset of RefSeq Curated, transcripts marked as RefSeq Select or MANE Select.
- A single Select transcript is chosen as representative for each protein-coding gene.
- This track includes transcripts categorized as MANE, they are further agreed upon as representative by both NCBI
- RefSeq and Ensembl/GENCODE, and have a 100% identical match to a transcript in
- the Ensembl annotation. See RefSeq Select+MANE (subset) – Subset of RefSeq Curated, transcripts marked as
+ RefSeq Select or MANE Select.
+ A single Select transcript is chosen as representative for each protein-coding gene.
+ This track includes transcripts categorized as MANE, which are further agreed upon as
+ representative by both NCBI RefSeq and Ensembl/GENCODE, and have a 100% identical match
+ to a transcript in the Ensembl annotation. See NCBI RefSeq Select.
- Note that we provide a separate track MANE,
- which contains only the MANE transcripts, and not the ones specific to RefSeq.
+ Note that we provide a separate track, MANE (hg38),
+ which contains only the MANE transcripts.
-
RefSeq HGMD (subset) – Subset of RefSeq Curated, transcripts annotated by the Human
Gene Mutation Database. This track is only available on the human genomes hg19 and hg38.
It is the most restricted RefSeq subset, targeting clinical diagnostics.
The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq HGMD,
RefSeq Select/MANE and UCSC RefSeq tracks follow the display conventions for
gene prediction tracks.
The color shading indicates the level of review the RefSeq record has undergone:
@@ -192,31 +194,31 @@
target="_blank">downloads server for local processing. You can also access any RefSeq table
entries in JSON format through our
JSON API.
The data in the RefSeq Other and RefSeq Diffs tracks are organized in
bigBed file format; more
information about accessing the information in this bigBed file can be found
below. The other subtracks are associated with database tables as follows:
- genePred format:
- RefSeq All - ncbiRefSeq
- RefSeq Curated - ncbiRefSeqCurated
- RefSeq Predicted - ncbiRefSeqPredicted
- RefSeq HGMD - ncbiRefSeqHgmd
- - RefSeq Select/MANE - ncbiRefSeqSelect
+ - RefSeq Select+MANE - ncbiRefSeqSelect
- UCSC RefSeq - refGene
- PSL format:
- RefSeq Alignments - ncbiRefSeqPsl
The first column of each of these tables is "bin". This column is designed
to speed up access for display in the Genome Browser, but can be safely ignored in downstream
analysis. You can read more about the bin indexing system
here.
The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed
files, which can be obtained from our downloads server here,