######################RAISE is used to circRNA ReAlign Inner Splice and Expression (RAISE) for circRNA backsplice sites identification, quantification of abundance and prediction of their internal structure using RNA-seq data.

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RAISE

Contains the following files:

• pipeline_prepare.txt
• pipeline_4tools_align.bash
• pipeline_main_abundance.bash
• acfs_example.txt
• put_together_ws.pl

four circRNA detection tools

• find_circ
• mapsplice (2.1.8)
• acfs
• circRNA_finder

These scripts have been tested on various Linux distributions. Before they can be run, make sure that the following prerequisites are installed:

• perl
• awk
• STAR (versions 2.3.1)
• samtools (1.3)
• bwa (0.7.3)
• hisat2 (2.0.4)
• bowtie2 (2.2.5)
• bedtools (2.24.0)
• stringtie (1.3.0)
• htseq-count (0.6.0)

To run the scripts to identify circular RNAs, first run hisat2 and STAR, once for each data set:

sh pipeline_4tools_align.bash

Next, run the post processing scripts:

sh pipeline_main_abundance.bash

For each library the following output files or folds are produced:

folds: a) <lib_name>_fc: find_circ output b) <lib_name>_acfs: acfs output c) <lib_name>_mapsplice: mapsplice output d) circRNA_validation: circRNA realignment details files: a) _filteredJunctions.bed: circRNA_finder output b) _total.txt: circRNA abundance b) _total.txt: circRNA abundance detail

any suggestion and question are welcome. email: [email protected]