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

Database: dm6 Primary Table: tss_RAMPAGE_Dmel09_E09h Data last updated: 2021-04-19
Big Bed File: /gbdb/dm6/bbi/RAMPAGE_dedup/tsrchitect/Dmel09_E09h_tsrchitect.bb
Item Count: 10,888
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_1448	Name of RAMPAGE peak
`score`	210	Score from 0-1000
`strand`	-	+ or -
`nTSSs`	12	Count of TSSs
`nTAGs`	6053	Count of tags
`tsrPeak`	0.21	Maximum tag count fraction for all TSS positions in the TSR
`tsrWdth`	52	Width of TSR
`tsrTrq`	-18.34	TSR torque; measure of TSR balance
`tsrSI`	-0.68	Shape index (SI) value of TSR
`tsrMSI`	0.25	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_1448	210	-	12	6053	0.21	52	-18.34	-0.68	0.25
chr2L	15748091	15748157	tsr_peaked_1449	440	-	10	784	0.44	66	-3.15	-0.74	0.17
chr2L	15751027	15751075	tsr_peaked_1450	230	-	9	708	0.23	48	12.31	-0.87	0.10
chr2L	15751094	15751110	tsr_peaked_1451	540	-	2	56	0.54	16	-0.54	1.00	0.00
chr2L	15752264	15752296	tsr_peaked_624	590	+	5	517	0.59	32	8.06	0.23	0.24
chr2L	15762435	15762436	tsr_peaked_1452	1000	-	1	39	1.00	1	0.00	2.00	1.00
chr2L	15762749	15762756	tsr_peaked_1453	390	-	3	142	0.39	7	1.02	0.43	0.01
chr2L	15764230	15764238	tsr_peaked_625	650	+	2	100	0.65	8	-1.05	1.07	0.07
chr2L	15764259	15764260	tsr_peaked_626	1000	+	1	36	1.00	1	0.00	2.00	1.00
chr2L	15768287	15768325	tsr_peaked_1454	410	-	4	155	0.41	38	-0.65	0.09	0.05

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