MacAulayLab Nocturnal rythem RNAseq

The work and scripts are done by the MacAulay Lab.
All programs used are free and open-source. In the interest of open science and reproducibility, all data and source code used in our research is provided here.
Feel free to copy and use code, but please cite:
(coming soon)
Remember rewrite file_names and folder_names suitable for your pipeline.
Note: Many of the tables output have converted dot to comma for danish excel annotation.

The RNAseq and Analysis follows these steps:

Raw data analysis - Library Build, Mapping and Quantification

The analysis uses RNA STAR for mapping and RSEM for TPM quantification.

RNA-STAR and RSEM Library build and indexing

1.1.1 - RNA_STAR_Indexing.sh
1.2.1 - RSEM_Indexing.sh

RNA-STAR Mapping and RSEM quantification

1.1.2 -RNA_STAR_RNAseq2.sh
1.2.2 - RSEM_RNAseq2.sh

Generate count table

2.1.1 - Generate count table from raw data.py

Generate overview table and overview table of transport

Requirements: Metadata table of transport (example in script).

3.1.1 - Overview table of light and dark phase