This repository contains the key files and analysis processes required for the stripe seq process for soybeans
- The 01Preprocessing_and_mapping.sh script covers the main steps from the fastq file to the downstream analysis.
- The 02CAGEfightR_for_downstream_analysis.ipynb file is actually a series of R commands for the downstream analysis process.
You can arrange your data according to the directory structure in the warehouse for repeatable analysis.
Note: Because the original sequencing data and genome files are too large, we have not saved them here. If necessary, the corresponding genome files can be downloaded from the Phytozome database here.
Xutong Wang, Jingbo Duan, Chancelor B. Clark, Wanjie Feng, Jianxin Ma(2024). Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin in soybean. https://www.biorxiv.org/content/10.1101/2024.03.27.587116v1.
Wang, X., Duan, J., Clark, C. B., Feng, W., & Ma, J. (2024). Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants. The Plant Cell, koae288. https://academic.oup.com/plcell/advance-article/doi/10.1093/plcell/koae288/7900478