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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel14_E14h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel14_E14h_tsrchitect.bb
Item Count: 8,811
Format description: RAMPAGE Peaks Identified by TSRchitect

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731775	Start position in chromosome
`chromEnd`	15731781	End position in chromosome
`name`	tsr_peaked_1223	Name of RAMPAGE peak
`score`	310	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	4	Count of TSSs
`nTAGs`	223	Count of tags
`tsrPeak`	0.31	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	6	Width of TSR
`tsrTrq`	0.59	TSR torque; measure of TSR balance
`tsrSI`	0.03	Shape index (SI) value of TSR
`tsrMSI`	0.01	Modified shape index (MSI) value of TSR

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	nTSSs	nTAGs	tsrPeak	tsrWdth	tsrTrq	tsrSI	tsrMSI
chr2L	15731775	15731781	tsr_peaked_1223	310	-	4	223	0.31	6	0.59	0.03	0.01
chr2L	15748122	15748123	tsr_peaked_1224	1000	-	1	71	1.00	1	0.00	2.00	1.00
chr2L	15751035	15751036	tsr_peaked_1225	1000	-	1	35	1.00	1	0.00	2.00	1.00
chr2L	15751067	15751075	tsr_peaked_1226	550	-	2	55	0.55	8	-0.32	1.01	0.01
chr2L	15752293	15752294	tsr_peaked_538	1000	+	1	74	1.00	1	0.00	2.00	1.00
chr2L	15762749	15762750	tsr_peaked_1227	1000	-	1	26	1.00	1	0.00	2.00	1.00
chr2L	16049992	16049995	tsr_peaked_539	540	+	2	307	0.54	3	0.08	1.00	0.00
chr2L	16165829	16165830	tsr_peaked_540	1000	+	1	49	1.00	1	0.00	2.00	1.00
chr2L	16168342	16168343	tsr_peaked_541	1000	+	1	61	1.00	1	0.00	2.00	1.00
chr2L	16251772	16251773	tsr_peaked_1228	1000	-	1	35	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