This repository contains code for the design, analysis, and evaluation of a library of 3'UTRs containing miRNA target sites. [ADD LINK ONCE THE PAPER IS PUBLISHED]
Evaluate the raw sequencing data to get counts and stabilities per construct.
- BWA-MEM
- PyDESeq2
- Download the data from GEO.
- Set library names individually in each file (list at the top).
- Extract the UMI from the reads and add it to the title:
python 1_split_UTR_rem_UMIs.py - Generate reference files:
- Use
2_ref_to_fasta.ipynb
- Use
- Index reference files:
bwa index ./3UTR/references_3UTR.fasta - Align to the reference:
nohup python3 -u 3_align_to_references.py > 3_align_to_references.txt & - Filter alignments:
nohup python3 -u 4_filter_alignments.py > 4_filter_alignments.txt & - Sort and index:
python 5_index_and_sort.py - UMI deduplication:
python 6_deduplicate_umis.py - Count alignments:
python 7_count_alignments.py - Process count data with PyDESEQ2:
- Use
8_compute_lfc_DESeq2.ipynb
- Use
Note: This process can also be run using a script in the folder. Set library names and generate index files before running.
Contains code for the design of library 2 and some analysis code for library 1 measurements.
Code to generate all figures and analyses used in the paper.
To generate the paper figures:
- Run the notebooks in order.
- Some notebooks may need to be run multiple times or in a different order. This is indicated in the notebooks where necessary.