Schema for MachiBase TSS Read Density - MachiBase Read Density for Different Developmental Stages
  Database: dm6    Primary Table: MachiBase_young_male_CTSS_plus    Row Count: 1   Data last updated: 2022-10-20
fieldexampleSQL type info
fileName /gbdb/dm6/bbi/MachiBase/you...varchar(255) values

This table points to a file in BigWig format.

Sample Rows
 
fileName
/gbdb/dm6/bbi/MachiBase/young_male_CTSS_normalized_plus.bw

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

MachiBase TSS Read Density (tss_MachiBase) Track Description
 

Description

These tracks show the normalized density of SAGE reads from different developmental stages of D. melanogaster. The datasets were produced by MachiBase and obtained from the NCBI BioProject database under the accession number PRJNA79391.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa and the alignment results were analyzed by CAGEr. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.05, T = 1*10^6

Credits

Ahsan B, Saito TL, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S. MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res. 2009 Jan;37(Database issue):D49-53.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.