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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel23_E23h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel23_E23h_tsrchitect.bb
Item Count: 3,289
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	16251772	Start position in chromosome
`chromEnd`	16251776	End position in chromosome
`name`	tsr_peaked_447	Name of RAMPAGE peak
`score`	730	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	2	Count of TSSs
`nTAGs`	110	Count of tags
`tsrPeak`	0.73	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	4	Width of TSR
`tsrTrq`	0.68	TSR torque; measure of TSR balance
`tsrSI`	1.15	Shape index (SI) value of TSR
`tsrMSI`	0.15	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
chr2L	16251772	16251776	tsr_peaked_447	730	-	2	110	0.73	4	0.68	1.15	0.15
chr2L	16261692	16261693	tsr_peaked_448	1000	-	1	50	1.00	1	0.00	2.00	1.00
chr2L	16287727	16287728	tsr_peaked_449	1000	-	1	25	1.00	1	0.00	2.00	1.00
chr2L	16302914	16302915	tsr_peaked_450	1000	-	1	38	1.00	1	0.00	2.00	1.00
chr2L	16307371	16307372	tsr_peaked_201	1000	+	1	26	1.00	1	0.00	2.00	1.00
chr2L	16310691	16310711	tsr_peaked_451	700	-	2	108	0.70	20	-3.87	1.12	0.12
chr2L	16325613	16325614	tsr_peaked_452	1000	-	1	37	1.00	1	0.00	2.00	1.00
chr2L	16352600	16352601	tsr_peaked_453	1000	-	1	77	1.00	1	0.00	2.00	1.00
chr2L	16352620	16352621	tsr_peaked_454	1000	-	1	82	1.00	1	0.00	2.00	1.00
chr2L	16447337	16447338	tsr_peaked_202	1000	+	1	40	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