Subtracks⇓  Description⇓  MachiBase TSS Read Density Track Settings
 
MachiBase Read Density for Different Developmental Stages   (All Expression and Regulation tracks)

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Track height: pixels (range: 11 to 110)
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List subtracks: only selected/visible    all    (14 of 14 selected)  
 
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 Larva (Minus)  MachiBase Read Density for Larva (Minus)   Schema 
 
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 Young Female (Plus)  MachiBase Read Density for Young Female (Plus)   Schema 
 
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 Young Female (Minus)  MachiBase Read Density for Young Female (Minus)   Schema 
 
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 Young Male (Plus)  MachiBase Read Density for Young Male (Plus)   Schema 
 
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 Young Male (Minus)  MachiBase Read Density for Young Male (Minus)   Schema 
 
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 Old Female (Plus)  MachiBase Read Density for Old Female (Plus)   Schema 
 
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 Old Female (Minus)  MachiBase Read Density for Old Female (Minus)   Schema 
 
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 Old Male (Plus)  MachiBase Read Density for Old Male (Plus)   Schema 
 
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 Old Male (Minus)  MachiBase Read Density for Old Male (Minus)   Schema 
    14 of 14 selected

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.

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