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Hi egaffo,
I'm trying to run circompara on my samples, but I got the following error:
finished circRNA detection from file samples/S1/processings/circRNAs/star_out/Chimeric.out.junction
dcc_fix_s…
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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 is any way to help me gen…
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Hi,
is there any option to save mapped reads? So, we could display the circRNA reads on IGV.
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Hi Egaffo, I have the following error:
"[SEGEMEHL] Fri Dec 29 08:21:58 2023: starting 65 threads.
[SEGEMEHL] Fri Dec 29 18:04:02 2023: threaded matching w/ suffixarray has taken 34924.000000 seconds…
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Hi Kipp,
I have met another issue when I analyzed my data (stranded total RNA-Seq) from FASTQ files. Only 9 circRNAs were detected but previously using BAMs as the starting point I found more than …
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I wonder if it is possible to include a new circRNA database (such as circAtlas). And in case of yes, which information it will be needed for that and which are the steps.
Thanks!
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Hi TreesLab,
Thanks for creating such an awesome tool. I wonder for the "start coordinate `pos1`" in `CIRC_FILE`, which system should the annotation be in? Each circle tool report the start coordin…
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Dear Professor,
Hello, thank you for your team's development of CIRIquant, an excellent tool. I have a question that needs your help. I want to know how to obtain the mature full-length sequence of…
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I try to use Clirc and I have a problem in the first step. When I try to extract circRNA sequences from my file with coordinates and reference genome that were used to detect circRNA i have the follow…
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Hi,
Thanks for CLEAR.
I am in troubles using CLEAR and looking for solutions. I need your help and this is the error log.
```bash
###Parameters:
Namespace(bowtie1='/home/ionadmin/likun…