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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel17_E17h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel17_E17h_tsrchitect.bb
Item Count: 10,976
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731780	Start position in chromosome
`chromEnd`	15731781	End position in chromosome
`name`	tsr_peaked_1508	Name of RAMPAGE peak
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	1	Count of TSSs
`nTAGs`	28	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	15731780	15731781	tsr_peaked_1508	1000	-	1	28	1.00	1	0.00	2.00	1.00
chr2L	15748122	15748123	tsr_peaked_1509	1000	-	1	49	1.00	1	0.00	2.00	1.00
chr2L	15751033	15751075	tsr_broad_67	240	-	11	956	0.24	42	3.50	-1.03	0.12
chr2L	15751094	15751095	tsr_peaked_1510	1000	-	1	33	1.00	1	0.00	2.00	1.00
chr2L	15752264	15752294	tsr_peaked_668	640	+	3	195	0.64	30	5.74	0.69	0.17
chr2L	15762749	15762750	tsr_peaked_1511	1000	-	1	53	1.00	1	0.00	2.00	1.00
chr2L	15764230	15764231	tsr_peaked_669	1000	+	1	45	1.00	1	0.00	2.00	1.00
chr2L	15768300	15768301	tsr_peaked_1512	1000	-	1	36	1.00	1	0.00	2.00	1.00
chr2L	16049992	16049995	tsr_peaked_670	580	+	2	247	0.58	3	-0.16	1.02	0.02
chr2L	16165829	16165830	tsr_peaked_671	1000	+	1	38	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