CIRCexplorer2
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YangLab
circular RNA analysis toolset
Hello, I am having trouble to find documentation about the circularRNA_known.txt table that circexplorer2 outputs. Each row gives information about one particular isoform. For example, it can tell you that...
I have got "IndexError: list index out of range" error when I run CIRCexplorer2. I used "fast_circ.py parse -r '/home/jaber/Desktop/volox/ncbi_dataset/data/GCA_000143455.1/genepred.txt' -g '/home/jaber/Desktop/volox/ncbi_dataset/data/GCA_000143455.1/GCA_000143455.1_v1.0_genomic.fna' -t TopHat-Fusion -o '/home/jaber/Desktop/volox/fast_circ' '/home/jaber/Desktop/volox/tophat2/accepted_hits.bam' " command. Does...
Hi, Thanks for this great tool. The **CIRCexplorer2 align** only supports single-end read data. The documentation mentioned **It is recommended to convert paired-end RNA-seq to single-read RNA-seq before alignment.** Can...
The reason I ran circexplorer2 is to know if the RNA contains any Fusions which are circular in nature. So in the Output of Circexplorer2 Annotate command, I see only...
When I ran CIRCxplorer2, it took me an over night to align the paired sequencing data using tophat. And then it took nearly 10 hours to go to the assembly...
Hey, Thanks for sharing this amazing tool! I found that **chrMT** appears in the .bed and .junction files, but not in the final counts table. I was wondering if there...
When running "fast_circ.py denovo" from the latest version of CIRCexplorer2, I encountered the following error: ``` Traceback (most recent call last): File "/mnt/lustre/shelkmike/Work/Tools/Anaconda/bin/fast_circ.py", line 8, in sys.exit(main()) File "/mnt/lustre/shelkmike/Work/Tools/Anaconda/lib/python3.9/site-packages/circ2/fast_circ.py", line...
Hi there, I'd like to try using CIRCexplorer2 to map circRNA reads in human genome. But since my project has over 1000 samples and we've already done the alignment work...
