This repository documents the analysis performed for The impact of sex on alternative splicing;
- Get access to the Genotype-Tissue Expression (GTEx) RNAseq data (an application to dbGAP for access to the dataset phs000424.v8.v2 is required)
- Search through the gen3.anvil.io/explorer.
- Search for the Transcriptome sequencing data
- Obtain using the GA4GH FASP scripts to obtain the aligned bam files
- Convert those files to fastq's to prep for re-alignment
and then continue with the previous step 2, now step 6
- Align each RNAseq sample using hisat2 and create a matrix of counts for each of a variety of splicing types was generated by the rMATS. Specifically, rMATS was run as a nextflow script. The script may be modified to run on any platform, the results from this study was performed on the cloudOS/lifebit platform.
- Run the Jupyter notebooks from this repository to perform the individual analyses.