Schema for TSRchitect Combined RAMPAGE TSS - TSRchitect Combined RAMPAGE Transcription Start Sites

Database: DpseGB3 Primary Table: tss_RAMPAGE2_star_Peaks Data last updated: 2019-07-07
Big Bed File: /gbdb/DpseGB3/bbi/RAMPAGE2_star/DpseGB3_tsrchitectPeaks.bb
Item Count: 17,096
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	CH379058	Reference sequence chromosome or scaffold
`chromStart`	3566112	Start position in chromosome
`chromEnd`	3566113	End position in chromosome
`name`	tsr_peaked_453	Name of RAMPAGE peak
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	1	Count of TSSs
`nTAGs`	30	Count of tags
`tsrPeak`	1	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	1	Width of TSR
`tsrTrq`	0	TSR torque; measure of TSR balance
`tsrSI`	2	Shape index (SI) value of TSR
`tsrMSI`	1	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
CH379058	3566112	3566113	tsr_peaked_453	1000	-	1	30	1	1	0	2	1
CH379058	3567322	3567380	tsr_peaked_130	300	+	13	4159	0.3	58	-2.02	-0.73	0.26
CH379058	3568672	3568673	tsr_peaked_131	1000	+	1	30	1	1	0	2	1
CH379058	3572092	3572097	tsr_peaked_454	910	-	2	506	0.91	5	1.62	1.55	0.55
CH379058	3573615	3573667	tsr_peaked_132	260	+	8	4626	0.26	52	-11.68	-0.64	0.12
CH379058	3573836	3573879	tsr_peaked_133	310	+	5	324	0.31	43	6.12	-0.19	0.06
CH379058	3580991	3580999	tsr_peaked_134	380	+	4	956	0.38	8	-0.35	0.11	0.06
CH379058	3581258	3581260	tsr_peaked_135	500	+	2	445	0.5	2	0	1	0
CH379058	3583334	3583335	tsr_peaked_136	1000	+	1	296	1	1	0	2	1
CH379058	3583389	3583390	tsr_peaked_137	1000	+	1	32	1	1	0	2	1

TSRchitect Combined RAMPAGE TSS (tss_RAMPAGE2_star_Combined) Track Description


	Description This track shows the locations of putative Transcription Start Sites (TSS) in the D. pseudoobscura genome based on the analysis of RAMPAGE results from multiple developmental stages of D. pseudoobscura embryos. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE89300. The RAMPAGE reads were mapped against the D. pseudoobscura (DpseGB3) assembly using STAR. The putative promoter regions were identified by TSRchitect. References Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6.

Description

References