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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel11_E11h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel11_E11h_tsrchitect.bb
Item Count: 7,188
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731775	Start position in chromosome
`chromEnd`	15731796	End position in chromosome
`name`	tsr_peaked_1041	Name of RAMPAGE peak
`score`	260	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	6	Count of TSSs
`nTAGs`	1080	Count of tags
`tsrPeak`	0.26	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	21	Width of TSR
`tsrTrq`	-6.39	TSR torque; measure of TSR balance
`tsrSI`	-0.38	Shape index (SI) value of TSR
`tsrMSI`	0.08	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
chr2L	15731775	15731796	tsr_peaked_1041	260	-	6	1080	0.26	21	-6.39	-0.38	0.08
chr2L	15748122	15748123	tsr_peaked_1042	1000	-	1	41	1.00	1	0.00	2.00	1.00
chr2L	15751035	15751036	tsr_peaked_1043	1000	-	1	34	1.00	1	0.00	2.00	1.00
chr2L	15751067	15751075	tsr_peaked_1044	510	-	2	86	0.51	8	-0.08	1.00	0.00
chr2L	15752274	15752294	tsr_peaked_441	810	+	2	134	0.81	20	5.81	1.29	0.29
chr2L	16049992	16049995	tsr_peaked_442	520	+	2	281	0.52	3	-0.05	1.00	0.00
chr2L	16168342	16168343	tsr_peaked_443	1000	+	1	32	1.00	1	0.00	2.00	1.00
chr2L	16257587	16257601	tsr_peaked_1045	430	-	3	136	0.43	14	0.08	0.46	0.03
chr2L	16261675	16261723	tsr_peaked_1046	550	-	5	346	0.55	48	-3.02	0.13	0.19
chr2L	16287727	16287732	tsr_peaked_1047	580	-	2	337	0.58	5	-0.33	1.02	0.02

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