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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel22_E22h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel22_E22h_tsrchitect.bb
Item Count: 4,354
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15751035	Start position in chromosome
`chromEnd`	15751036	End position in chromosome
`name`	tsr_peaked_637	Name of RAMPAGE peak
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	1	Count of TSSs
`nTAGs`	27	Count of tags
`tsrPeak`	1.00	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	1	Width of TSR
`tsrTrq`	0.00	TSR torque; measure of TSR balance
`tsrSI`	2.00	Shape index (SI) value of TSR
`tsrMSI`	1.00	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
chr2L	15751035	15751036	tsr_peaked_637	1000	-	1	27	1.00	1	0.00	2.00	1.00
chr2L	15751067	15751068	tsr_peaked_638	1000	-	1	28	1.00	1	0.00	2.00	1.00
chr2L	15752293	15752294	tsr_peaked_266	1000	+	1	28	1.00	1	0.00	2.00	1.00
chr2L	16049994	16049995	tsr_peaked_267	1000	+	1	29	1.00	1	0.00	2.00	1.00
chr2L	16168342	16168343	tsr_peaked_268	1000	+	1	45	1.00	1	0.00	2.00	1.00
chr2L	16251772	16251776	tsr_peaked_639	590	-	2	93	0.59	4	0.27	1.02	0.02
chr2L	16261692	16261693	tsr_peaked_640	1000	-	1	58	1.00	1	0.00	2.00	1.00
chr2L	16287727	16287732	tsr_peaked_641	690	-	2	96	0.69	5	-0.75	1.10	0.10
chr2L	16302914	16302915	tsr_peaked_642	1000	-	1	42	1.00	1	0.00	2.00	1.00
chr2L	16307371	16307372	tsr_peaked_269	1000	+	1	33	1.00	1	0.00	2.00	1.00

TSRchitect RAMPAGE Embryos TSS (tss_RAMPAGE_embryos) Track Description


	Description This track shows the locations of putative Transcription Start Sites (TSS) in the D. melanogaster genome based on the analysis of RAMPAGE data from different embryonic stages in one-hour intervals. The embryos RAMPAGE datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession numbers GSE36212 and GSE89299. The RAMPAGE reads were mapped against the D. melanogaster (dm6) 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 P, Dobin A, Plessy C, Carninci P, Gingeras TR. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res. 2013 Jan;23(1):169-80.

Description

References