Schema for TSRchitect Combined RAMPAGE TSS (Replicate 1) - TSRchitect Combined RAMPAGE Transcription Start Sites (Replicate 1)

Database: dm6 Primary Table: tss_RAMPAGE_dedup_Peaks Data last updated: 2021-04-18
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/GSE36212/GSE36212_tsrchitectPeaks.bb
Item Count: 33,012
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15728940	Start position in chromosome
`chromEnd`	15728941	End position in chromosome
`name`	tsr_peaked_4352	Name of RAMPAGE peak
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	1	Count of TSSs
`nTAGs`	29	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	15728940	15728941	tsr_peaked_4352	1000	-	1	29	1.00	1	0.00	2.00	1.00
chr2L	15729141	15729156	tsr_peaked_4353	560	-	2	79	0.56	15	-0.80	1.01	0.01
chr2L	15729353	15729354	tsr_peaked_4354	1000	-	1	29	1.00	1	0.00	2.00	1.00
chr2L	15729454	15729455	tsr_peaked_4355	1000	-	1	35	1.00	1	0.00	2.00	1.00
chr2L	15729499	15729500	tsr_peaked_4356	1000	-	1	37	1.00	1	0.00	2.00	1.00
chr2L	15731768	15731860	tsr_peaked_4357	210	-	22	22768	0.21	92	-32.69	-0.86	0.36
chr2L	15743368	15743374	tsr_peaked_4358	500	-	2	62	0.50	6	0.00	1.00	0.00
chr2L	15745570	15745571	tsr_peaked_4359	1000	-	1	41	1.00	1	0.00	2.00	1.00
chr2L	15745841	15745842	tsr_peaked_1884	1000	+	1	54	1.00	1	0.00	2.00	1.00
chr2L	15746523	15746524	tsr_peaked_4360	1000	-	1	72	1.00	1	0.00	2.00	1.00

TSRchitect Combined RAMPAGE TSS (Replicate 1) (tss_RAMPAGE_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. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE36212. 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