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This package contains code to analyze RNA-seq data and generate figures and tables presented in:

Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies.
Shih MF*, Davis FP*, Henry GL+, Dubnau J+

Contact with any questions.

Package contents

  • src - code, organized by language, to turn RNA-seq read files into figures.
  • metadata - text tables describing RNA-seq samples
  • data - text data files used by code



The data used by this package comes from several sources. We include nearly all data files expected by the R and slurm shell programs, along with README files describing the contents. The only exceptions are large files (eg, genome sequence, gene annotations, transcript sequences, RNA-seq alignment indices), which we do not provide but describe in README files how to obtain or build.

Data Source
RNA-seq FASTQ files GEO accession GSE119629
genome sequence ENSEMBL release 91; based on BDGP6 (dm6)
gene structures ENSEMBL release 91; based on FlyBase 2017_04


We used the following software on the NIH Biowulf slurm-based linux cluster.

# Software Source
1 seqtk 1.2
2 kallisto 0.43.1
3 STAR 2.5.3a
4 picard 1.119
5 R v3.5.0
6 deeptools

Analysis overview

The analysis includes procerssing the RNA-seq reads and then generating figures and tables.

1. RNA-seq read processing

This step is implemented in a slurm script that trims the reads (seqtk), pseudo-aligns them to the transcriptome (kallisto) and aligns them to the genome (STAR), evaluates quality metrics (picard), and generates bigwig tracks for visualization (samtools, ucsc kent tools)


2. Generating figures and tables

An R script generates all the tables and figures in the manuscript.

dat <- main()