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data
metadata
src
README.md

README.md

mushroombody

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 fred.davis@nih.gov 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

Requirements

Data

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

Software

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

# Software Source
1 seqtk 1.2 https://github.com/lh3/seqtk
2 kallisto 0.43.1 https://pachterlab.github.io/kallisto/
3 STAR 2.5.3a https://github.com/alexdobin/STAR
4 picard 1.119 http://broadinstitute.github.io/picard/
5 R v3.5.0 https://www.r-project.org/
6 deeptools 2.5.0.1 https://deeptools.readthedocs.io/

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)

sbatch process_rnaseq_samples.slurm.sh

2. Generating figures and tables

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

source("../../src/R/analyzeKenyonTapinSeq_ms.R")
dat <- main()