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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel07_E07h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel07_E07h_tsrchitect.bb
Item Count: 9,608
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731773	Start position in chromosome
`chromEnd`	15731825	End position in chromosome
`name`	tsr_peaked_1314	Name of RAMPAGE peak
`score`	220	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	12	Count of TSSs
`nTAGs`	6899	Count of tags
`tsrPeak`	0.22	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	52	Width of TSR
`tsrTrq`	-18.00	TSR torque; measure of TSR balance
`tsrSI`	-0.76	Shape index (SI) value of TSR
`tsrMSI`	0.23	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
chr2L	15731773	15731825	tsr_peaked_1314	220	-	12	6899	0.22	52	-18.00	-0.76	0.23
chr2L	15746609	15746610	tsr_peaked_1315	1000	-	1	28	1.00	1	0.00	2.00	1.00
chr2L	15748091	15748157	tsr_peaked_1316	420	-	11	947	0.42	66	-0.61	-0.85	0.17
chr2L	15751035	15751075	tsr_peaked_1317	290	-	6	524	0.29	40	9.43	-0.48	0.04
chr2L	15752264	15752310	tsr_peaked_567	510	+	6	511	0.51	46	-0.03	-0.06	0.20
chr2L	15762749	15762750	tsr_peaked_1318	1000	-	1	42	1.00	1	0.00	2.00	1.00
chr2L	15764230	15764238	tsr_peaked_568	710	+	2	89	0.71	8	-1.46	1.13	0.13
chr2L	15764263	15764264	tsr_peaked_569	1000	+	1	34	1.00	1	0.00	2.00	1.00
chr2L	15768300	15768325	tsr_peaked_1319	470	-	3	116	0.47	25	-0.62	0.47	0.04
chr2L	16042921	16042922	tsr_peaked_570	1000	+	1	27	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