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It is believed that many inexperienced people have no idea about how to identify circular RNA in circRNA_finder. Therefore, this paper summarizes the causes and solutions of the problem. Through this article, I hope you can solve this problem.

1. STAR alignment reference genome

STAR is a transcriptome data comparison software that supports chimera comparison, that is, it supports the alignment of two parts of a reads to different genomic regions. The junction reads of circular RNA meets this requirement. The code is as follows

STAR\-- genomeDir hg19_star_db/\-- readFilesCommand gunzip-c\-- readFilesIn R1.fastq.gz R2.fastq.gz\-- runThreadN 4\-- chimSegmentMin 20\-- chimScoreMin 1\-- alignIntronMax 500000\-- outFilterMismatchNmax 4\-- alignTranscriptsPerReadNmax 100000\-- twopassMode Basic\-outSAMtype BAM SortedByCoordinate\-chimOutType SeparateSAMold\-- outFilterMultimapNmax 2\-- outFileNamePrefix C1

Although the software provides a script called runStar.pl, it is not easy to use because of the version of STAR. The script is essentially an encapsulation of STAR, just use STAR directly, and the parameters can be set by referring to the settings in the script.

two。 Run circRNA_finder

The second step is to predict the ring RNA, the code is as follows

Perl\ postProcessStarAlignment.pl\-- starDir star_out_dir\-- minLen 100-- outDir output_dir

After the run is complete, there will be three files with the corresponding suffix as follows

_ filteredJunctions.bed

_ s_filteredJunctions.bed

_ s_filteredJunctions_fw.bed

The first file is the result file of all annular RNA; the second file is the annular RNA; of which the shear site conforms to the GT-AG shearing signal. The third file has the same annular RNA as the second file, but the linear RNA average sequencing depth information near the annular RNA connection point is added. Normally, we select the result of the second file as the final annular RNA prediction result, which is shown below

After reading the above, have you mastered how to identify circular RNA in circRNA_finder? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!

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