#Educational_tool
#Introduction_of_find_circ_tool to identify #circRNA in the genome
This tool is introduced for the first time in this channel to serve dear companions.
One of the key and prominent analyzes in the evaluation of RNAseq sequences is the identification of circular RNA molecules that exist in the genome. For this, a tool called find_circ is needed to map the upcoming reads using the bowtie2 module and samtools and identify the target circRNA molecules for you based on the information contained in the genome sequence. To run this tool, users must install Python on their operating system. This software supports Python version 2.7, so when you run the find_circ.py script, you must have the Python 2.7 interpreter on your operating system. The channel admin has tested this tool with Python version 3, but it encounters an error when running, so it is better to use this tool with the same version 2.7. The method of working with this tool is simple. In this way, you first download the reference genome sequence from SRA, then in the next step, you clean or trim the target genome using trimming software. In the next step, the RNAseq reads after trimming should be mapped using tools such as topHat or STAR. After the mapping step, the resulting output should be applied to find_circ to identify circRNAs for you by processing the available information.
As mentioned, to work with find_circ, two tools, samtools and Bowtie2, must be installed on your operating system. For this purpose, you can download and install the find_circ tools and two required modules from the links below, and then process your transcriptomic information. :
1. http://samtools.sourceforge.net/
2. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
3. https://github.com/zagrosman/find_circ
Be careful that the find_circ tool is executed as a Python script, as a result, you must prepare a workfolder using the help file of the tool, then in the next step, put the primary files inside it and execute it step by step. Do the necessary processing with the relevant commands. This software is optimized for Linux environment.
For users who use Windows 10 or 11 environment, we recommend that they download the version of Ubuntu Windows version 21.10 and by activating the Windows Linux base without installing peripheral tools and virtual drives and directly installing Linux, they can benefit from the features of Linux in Windows. It is very easy to work with these platforms, you just have to be very patient and don’t lose your energy when facing terminal errors and solve the terminal problems with patience.
#Genomics
#Transcriptomics
#RNAseq
#mapper
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Virtual Research Institute of Bioinformatics and Pharmaceutical Biotechnology
#Bioinformatics
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This post is written by NBICS_2024