CIRCexplorer2
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YangLab
circular RNA analysis toolset
Hello I want to use circExplorer2 for the rat (Rattus novergicus) dataset. I was trying to fetch the rat genome using the command: fetch_ucsc.py Rnor_6.0 fa Rn6.fa it's giving me...
Hi The annotate step need this file hg19_ref_all.txt, I want to know is that file representing the human GTF file? or how I can generate the file (hg19_ref_all.txt)
I wanted to run the parse module. I have used the same command as suggested by manual (CIRCexplorer2 parse --pe -t TopHat-Fusion tophat_fusion/accepted_hits.bam > CIRCexplorer2_parse.log). However, my log file is...
hey i m using circexplorer2 for circular RNA detection in solanum lycopersicum for that how may I generate the .refFlat file for solanum lycopersicum or ref.txt file so that i...
Hi, my task is to compute the coverage from the tophat2 accepted_hits.bam with the back_spliced_junction.bed, but I don´t know if the results I got from... samtools depth -H -o Coverage/cov_TT17...
Hi @kepbod, I found one of my datasets (phs001680/PRJNA48954) didn't convert any fusion reads! my code is: ```` CIRCexplorer parameters: /home/zhou/miniconda2/envs/cir2/bin/CIRCexplorer2 parse -t STAR /home/zhou/raid/ncbi/dbGaP-24835/RNA_phs001680_PRJNA489548/CircRNA/STAR/SRR8992923/SRR8992923_Chimeric.out.junction -b /home/zhou/raid/ncbi/dbGaP-24835/RNA_phs001680_PRJNA489548/CircRNA/parse/SRR8992923_back_spliced_junction.bed Start CIRCexplorer2 parse...
I parse my STAR chimeric junction file to detect circRNAs using CIRCExplorer2. It generates a backspliced_junctions.bed file. How do I get the readids supporting the backspliced junctions so that I...
Hello, Thanks so much for developing this wonderful tool! I would like to confirm if my interpretation of circExplorer2-reported circRNA coordinates are correct? So after a few manual inspections of...
For instance, let's say that my reads per gene contains the following information for these two transcripts (Reads per gene file obtained with STAR): ``` **ENST00000361204** 0 0 **0** **ENST00000255784**...
Hello.. I am currently having an issue with the annotation part. I am using Linux to perform CIRCexplorer2 analysis. After aligning everything with STAR as described by you, for instance:...