Schema for TSRchitect Combined RAMPAGE TSS (Replicate 2) - TSRchitect Combined RAMPAGE Transcription Start Sites (Replicate 2)

Database: dm6 Primary Table: tss_RAMPAGE2_dedup_Peaks Data last updated: 2021-04-18
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/GSE89299/GSE89299_tsrchitectPeaks.bb
Item Count: 25,501
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15728320	Start position in chromosome
`chromEnd`	15728321	End position in chromosome
`name`	tsr_peaked_3174	Name of RAMPAGE peak
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	1	Count of TSSs
`nTAGs`	37	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	15728320	15728321	tsr_peaked_3174	1000	-	1	37	1.00	1	0.00	2.00	1.00
chr2L	15729077	15729080	tsr_peaked_3175	530	-	2	53	0.53	3	-0.06	1.00	0.00
chr2L	15729109	15729110	tsr_peaked_3176	1000	-	1	26	1.00	1	0.00	2.00	1.00
chr2L	15729129	15729156	tsr_peaked_3177	470	-	5	289	0.47	27	0.55	-0.01	0.13
chr2L	15729297	15729298	tsr_peaked_3178	1000	-	1	31	1.00	1	0.00	2.00	1.00
chr2L	15729348	15729354	tsr_peaked_3179	520	-	2	120	0.52	6	0.08	1.00	0.00
chr2L	15729499	15729500	tsr_peaked_3180	1000	-	1	38	1.00	1	0.00	2.00	1.00
chr2L	15731768	15731825	tsr_peaked_3181	250	-	14	11816	0.25	57	-15.93	-0.74	0.28
chr2L	15745841	15745842	tsr_peaked_1366	1000	+	1	66	1.00	1	0.00	2.00	1.00
chr2L	15746513	15746525	tsr_peaked_3182	470	-	3	140	0.47	12	2.28	0.47	0.04

TSRchitect Combined RAMPAGE TSS (Replicate 2) (tss_RAMPAGE2_dedup_Combined) 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 results from multiple developmental stages of D. melanogaster embryos. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number 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 PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6. 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