These scripts are used in the analysis of RNA secondary structure bias for the real edited A sites and random A sites in Fusarium graminearum, which firstly conducted in our RNA editing paper[1].
.
|-- README.md # This file
|-- data # Data directory
| |-- 3-30.txt # Edited A sites (upstream 30 nt + A + downstream 30 nt) in F. graminearum [editing level: 3-30%]
| |-- 30-60.txt # Edited A sites (upstream 30 nt + A + downstream 30 nt) in F. graminearum [editing level: 30-60%]
| |-- 60-100.txt # Edited A sites (upstream 30 nt + A + downstream 30 nt) in F. graminearum [editing level: 60-100%]
| |-- Sex8d.flank30.fa # Edited A sites (upstream 30 nt + A + downstream 30 nt) in F. graminearum [editing level: 3-100%]
| `-- fg.sample.1.fa # Random A sites (upstream 30 nt + A + downstream 30 nt) in F. graminearum
|-- dotbracket_to_element_string.py # Python script which converts a dotbracket notation to an element-type notation, form forgi package
|-- mfe.R # R script used to generate MFE plot
|-- mfe.sh # Shell script used to extract MFE from the *.str.txt files
|-- mfe_hairpin_loop.R # R script used to generate MFE plot - hairpin
|-- mfe_hairpin_loop.sh # Shell script used to extract MFE from the *.str.txt files - hairpin
|-- output # Output directory
| |-- bg.dat # Background (random A sites), MFE - all
| |-- bg.h.dat # Background (random A sites), MFE - hairpin
| |-- bg.stats.txt # Background (random A sites), secondary structure summary
| |-- bg.str.txt # Background (random A sites), secondary structure - detail (structure and MFE)
| |-- class.dat # Automatically generated RNA secondary structure classification file
| |-- class.freq # Manually adjusted RNA secondary structure classification file
| |-- ed.dat # Edited A sites, MFE - all [editing level: 3-100%]
| |-- ed.h.dat # Edited A sites, MFE - hairpin [editing level: 3-100%]
| |-- ed.stats.txt # Edited A sites, secondary structure summary [editing level: 3-100%]
| |-- ed.str.txt # Edited A sites, secondary structure - detail (structure and MFE) [editing level: 3-100%]
| |-- ed100.dat # Edited A sites, MFE - all [editing level: 60-100%]
| |-- ed100.h.dat # Edited A sites, MFE - hairpin [editing level: 60-100%]
| |-- ed100.stats.txt # Edited A sites, secondary structure summary [editing level: 60-100%]
| |-- ed100.str.txt # Edited A sites, secondary structure - detail (structure and MFE) [editing level: 60-100%]
| |-- ed30.dat # Edited A sites, MFE - all [editing level: 3-30%]
| |-- ed30.h.dat # Edited A sites, MFE - hairpin [editing level: 3-30%]
| |-- ed30.stats.txt # Edited A sites, secondary structure summary [editing level: 3-30%]
| |-- ed30.str.txt # Edited A sites, secondary structure - detail (structure and MFE) [editing level: 3-30%]
| |-- ed60.dat # Edited A sites, MFE - all [editing level: 30-60%]
| |-- ed60.h.dat # Edited A sites, MFE - hairpin editing level: 30-60%]
| |-- ed60.stats.txt # Edited A sites, secondary structure summary editing level: 30-60%]
| |-- ed60.str.txt # Edited A sites, secondary structure - detail (structure and MFE) editing level: 30-60%]
| |-- mfe.pdf # MFE plot
| `-- stack.pdf # Stack plot
|-- run.sh # Shell script used to generate the secondary structure summary file
|-- stack.sh # Shell script used to generate the output/class.dat file
|-- stackstr.R # R script used to produce the stack plot
`-- structure_bias.pl # Perl script used to calculate the RNA secondary structure of the given sequences
For newly generated data, please run structure_bias.pl firstly and then use *.R for plots.
[1]: Liu H, Wang Q, He Y, Chen L, Hao C, Jiang C, Li Y, Dai Y, Kang Z, Xu JR. (2016) Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes. Genome Res 26, 449-509.