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- [x] remove Alignment folder.
- [x] remove circRNA_Identification/Mapsplice/*output_mapsplice. They are temp files.
- [x] output re-quantitve result for each sample.
- [x] star output samfiles ar…
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Hi guys,
I got an new error when running the command: `java -jar /opt/biosoft/CIRI-full_v2.0/CIRI-vis_v1.4.jar -i out_merge_circRNA_detail.anno -l output_library_length.list -r zma_dna_v4.fa -min 1…
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Once the user identifies differentially expressed circRNA, how can the miRNA they interact with be predicted? The IDs given to the transcripts by CIRIquant are not in some standard format such as circ…
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Hi,
[CLEAR](https://github.com/YangLab/CLEAR) is a tools for circRNA quantification, and requires tophat2, but tophat2 requires python2. So there is a question.
1. I cannot run snakemake in the envi…
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Hi David,
Thank you for the updated code for the BS junction sequence. I still have a minor pb when using Ciri output as it uses bwa and not STAR there is a shift of one base that appears in the sequ…
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Hi, thank you for the tool.
I installed all required packages and dependencies on python3.6.0 and run the example test....all seems fine (fasta for circRNA generated and also the predictions with the…
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- switch modules to containers (#42)
- remove any biowulf-specific code from driver script
- remove hard-coded biowulf paths from config, or document them well
- test on FRCE to verify that it work…
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This error occur during circJuncDE script use:-
> CIRI.files=c("DS1.out","DS2.out","DS7.out","DS8.out")
> designs=c(0,0,1,1)
> fdr.level=0.05
res1=circJuncDE(CIRI.files[c(1,2,3,4)],designs,cir…
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Respected professor
As of now im just replicating your paper and file results and then I will produce results from my own data. In my root directory I have made a subdirectory called data in which …
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Hello,
I just tried out starchip. I have no problem with step 1
```
$ ./Step1.sh
Filtering out chimeric reads that appear circular
Filtering circular reads based on assigned thresholds of 5 r…