Shulou(Shulou.com)06/02 Report--

This article shows you how to use CIRI to identify ring RNA, the content is concise and easy to understand, can definitely brighten your eyes, through the detailed introduction of this article, I hope you can get something.

In the initial study of annular RNA, it is considered that annular RNA is formed by reverse shear of exon, which is called exonic circRNA. Only such annular RNA can be verified by PCR reaction.

CIRI is a circular RNA detection software. Through the prediction results of this software, scholars have verified intronic circRNA and intergenic circRNA by experiments for the first time. The software is easy to operate and has high accuracy. It is a very popular annular RNA detection software.

The software needs at least two input files, the fasta sequence of the genome and the sam file generated by sequencing data alignment. It should be noted that the input sam file must be generated by bwa-mem algorithm comparison. The pipeline of the analysis is as follows

The input sam file needs to be scanned twice. In the first scan, the candidate ring RNA is screened according to the comparison of the two-terminal data. This step is realized by judging the value of the column of CIGAR in the SAM file, which is essentially to detect the junction reads at the connection point of the ring RNA. According to the sequence reading length and the characteristics of the genome region included at the connection point, it is divided into the following three models

Figure A shows that junction read covers only part of the sequence of the starting exon and the terminating exon. The alignment positions of these two parts of reads in the genome are opposite, and most of the circular RNA are in accordance with this model.

Figure B shows that junction read not only covers the two parts of the initiation exon and the termination exon, but also covers the partial sequence of one exon in the middle, in which case the reads can be divided into three parts to compare to the genome.

Figure C shows that junction read not only covers the entire ring RNA, but also repeats and reads part of the sequence, which can only occur when the sequence length of the ring RNA is smaller than the sequence read length.

The software defines the above three models as paired chiastic clipping signals, or PCC signal for short. If the comparison of a reads accords with any of the above, the reads is considered to be the junction reads of a circular RNA.

In order to improve the accuracy, after the junciton reads is identified, it will also be filtered with the quality of double-terminal sequence alignment paired end mapping, that is, the conservative splice sites of PEM and GT-AG, as shown in the following diagram

Only the junciton reads with high alignment quality and AG-GT shearing signal at the head and tail is retained to enter the downstream analysis. In the process of scanning the SAM file for the second time, the final prediction result of the annular RNA is given by the dynamic programming algorithm. If the GTF file is provided, the annular RNA will be annotated.

The steps for using the software are as follows

1. Bwa alignment reference genome

The code is as follows

Bwa mem\-T 19\-t 5 hg19_index\ R1.fastq.gz R2.fastq.gz\ > align.sam2. Run CIRICIRI2.pl\-T 20\-F hg19.fa\-A hg19.gtf\-I align.sam\-O circRNA.xls

The output is as follows

In the follow-up verification, the ones with high expression can be selected to verify. In the corresponding articles of the software, the circular RNA with junction reads number greater than 5 is selected for verification.

The above is how to use CIRI to identify circular RNA. Have you learned any knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.