public interface TranscriptSupportLevels
6
is used as a substitute for
transcripts that are marked as primary in UCSC, 7
for the longest transcript (in absence of both level
and UCSC primary marking), and 8
for transcripts that fall neither into pseudo-level 6
and
7
. A value of -1
is used for N/A.Modifier and Type | Field and Description |
---|---|
static int |
LONGEST_TRANSCRIPT
Longest transcript of a gene (used in absence of any TSL annotation and UCSC annotation of this transcript).
|
static int |
LOW_PRIORITY
Lowest available priority (used in absence of any TSL and UCSC annotation of this transcript).
|
static int |
NOT_AVAILABLE
the transcript was not analyzed for one of the following reasons:
pseudogene annotation, including transcribed pseudogenes
human leukocyte antigen (HLA) transcript
immunoglobin gene transcript
T-cell receptor transcript
single-exon transcript (will be included in a future version)
|
static int |
TSL1
All splice junctions of the transcript are supported by at least one non-suspect mRNA.
|
static int |
TSL2
The best supporting mRNA is flagged as suspect or the support is from multiple ESTs.
|
static int |
TSL3
The only support is from a single EST.
|
static int |
TSL4
The best supporting EST is flagged as suspect.
|
static int |
TSL5
No single transcript supports the model structure.
|
static int |
UCSC_CANONICAL
Annotated as canonical transcript by UCSC (used in absence of TSL).
|
static final int NOT_AVAILABLE
static final int TSL1
static final int TSL2
static final int TSL3
static final int TSL4
static final int TSL5
static final int UCSC_CANONICAL
static final int LONGEST_TRANSCRIPT
static final int LOW_PRIORITY
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