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.
- 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 | 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/ |
The analysis includes procerssing the RNA-seq reads and then generating figures and tables.
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.shAn R script generates all the tables and figures in the manuscript.
source("../../src/R/analyzeKenyonTapinSeq_ms.R")
dat <- main()