CIRCshapemapper v2

CIRCshapemapper2 is a pipeline to analyze the circSHAPE-MaP data. Using this pipeline, you could produce a SHAPE reactivity file of circRNA, which was used for modeling RNA secondary structure.

A schematic flow shows the pipeline

Requirement

• ShapeMapper-2.1.3
  The requirement of ShapeMapper-2.1.3 installation please read the README.md in ShapeMapper2 package.
• python3

Install

Install ShapeMapper-2.1.3 first. please add PATH of shapemapper_mutation_counter and shapemapper_mutation_parser from ’/shapemapper-2.1.3/bin/‘ folder in your .bashrc or .profile

All add script of CIRCshapemapper v2 in your PATH. The file 'normalize_profiles.py' ,'make_reactivity_profiles.py' , 'tab_to_shape.py' and 'render_figures.py' are from shapemapper-2.1.3 .

Usage

CIRCshapemapper_V2.sh

Description: CIRCshapemapper version 2 pipeline. Merge two primer product sequences. Suit for single circRNA. multiple circRNAs should run respectively .

Usage:

CIRCshapemapper_V2.sh -f circRNA.fa -t circRNA -p  circPrimer.txt -P primer_pair -N NAI_R1.fastq -n NAI_R2.fastq -D DC_R1.fastq -d DC_R2.fastq -U DMSO_R1.fastq -u DMSO_R2.fastq -M 1000 -o outDir
Option:
-f     -- circRNA fa file
-t     -- target name in shape
-p     -- circRNA primer for trim;txt formate
-P     -- circRNA primer to generate new reference; txt formate
-N     -- NAI samples R1
-n     -- NAI samples R2
-D     -- Denatured samples R1
-d     -- Denatured samples R2
-U     -- Untreated sample R1
-u     -- Untreated sample R2
-M     -- min-deep default 1000
-o     -- output document
-v     -- verbose mode, output command but out execute
-h     -- help information

Version: 2.0

SM2_Trim_primer_v2_py3.py

	usage: Trim primers from alignment file [-h] [-i INPUT] [-p PRIMER] [-o OUT]
	optional arguments:
	-h, --help            show this help message and exit
	-i INPUT, --input INPUT sam file
	-p PRIMER, --primer PRIMER primer file 
	-o OUT, --out OUT    output file

File formate

-p filename -- circRNA primer for trim;txt formate each primer in one line, including forward primers and reverse primers

TGTGATGGGGACATTGTTAT

AACTTGCACCTGCCACAGTC

ACAGTGTGAGTGTGTCCTGCACAATA

ACAGTGGACCATGGGAGAATGCGGAC

ACAGTG is a barcode for separate data. If your primers don't contain a barcode, just recode your primer is ok.

-P primer_pair -- circRNA primer for generate new reference;txt formate include two files

primer_pair_F.txt

TGTGATGGGGACATTGTTAT

AACTTGCACCTGCCACAGTC

primer_pair_R.txt

TGAGTGTGTCCTGCACAATA

GACCATGGGAGAATGCGGAC

Citation

• Liu CX#, Li X#, Nan F#, Jiang S, Gao X, Guo SK, Xue W, Cui Y, Dong K, Ding H, Qu B, Zhou Z, Shen N*, Yang L* and Chen LL*. Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity. Cell, 2019, 177(4): 865-880.e21

• Guo SK#, Nan F#, Liu CX, Yang L and Chen LL*. Mapping circular RNA structures in living cells by SHAPE-MaP. Methods, 2021, 19647-55

License

Copyright (C) 2019 YangLab. Licensed GPLv3 for open source use or contact YangLab (yanglab@@picb.ac.cn) for commercial use.