Schema for TransDecoder Transcripts - Transcripts and Coding Regions Predicted by TransDecoder

Database: DvirCAF1 Primary Table: transdecoder Row Count: 28,864 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DvirCAF1_stringtie.5.1_m.7	`varchar(255)`	values
`chrom`	scaffold_10022	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	330	`int(10) unsigned`	range
`txEnd`	1004	`int(10) unsigned`	range
`cdsStart`	330	`int(10) unsigned`	range
`cdsEnd`	1003	`int(10) unsigned`	range
`exonCount`	3	`int(10) unsigned`	range
`exonStarts`	330,541,890,	`longblob`
`exonEnds`	486,833,1004,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DvirCAF1_stringtie.5.1_m.7	scaffold_10022	-	330	1004	330	1003	3	330,541,890,	486,833,1004,
585	DvirCAF1_stringtie.9.1_m.13	scaffold_10026	-	182	620	182	618	2	182,414,	323,620,
585	DvirCAF1_stringtie.13.1_m.18	scaffold_10036	-	380	990	380	989	1	380,	990,
585	DvirCAF1_stringtie.13.1_m.17	scaffold_10036	-	380	990	381	990	1	380,	990,
585	DvirCAF1_stringtie.15.1_m.20	scaffold_10047	+	0	308	0	306	1	0,	308,
585	DvirCAF1_stringtie.15.1_m.24	scaffold_10047	+	0	308	2	308	1	0,	308,
585	DvirCAF1_stringtie.19.1_m.25	scaffold_10060	-	29	818	30	816	2	29,758,	545,818,
585	DvirCAF1_stringtie.26.1_m.27	scaffold_10105	-	2	674	2	674	1	2,	674,
585	DvirCAF1_stringtie.40.1_m.31	scaffold_10191	+	16	1112	18	390	1	16,	1112,
585	DvirCAF1_stringtie.50.1_m.32	scaffold_10248	+	219	1346	219	980	3	219,500,913,	426,850,1346,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TransDecoder Transcripts (transdecoder) Track Description


	Description This track shows the RNA-Seq transcripts assembled by StringTie. Coding regions within the transcript are identified by TransDecoder. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the accession number SRP006203. Methods TransDecoder was run against the transcripts assembled by StringTie using default parameters. The open reading frames predicted by TransDecoder were searched against the Swiss-Prot database using NCBI blastp and against the Pfam database using HMMER. Open reading frames are kept if they satisfy the TransDecoder.Predict filtering criteria or if they show significant matches to either Swiss-Prot or Pfam. References Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5. Haas BJ et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23.

Description