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Hi kevin,
I'm not very clear the steps of "Generate RNase R effect corrected BSJ information" . Should I run CIRIquant with RNase R treated samples 2 times and add --RNaseR option with "the output …
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All circRNAs were labeled as "intergenic" when using GTF downloaded from UCSC table browser
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Hi I was trying to combine the results together. since there have have issue when I integrate those bam files together. Right now I have CircCoordinates CircRNACount CircSkipJunctions LinearCount F…
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Hello,
kallisto (0.44.0) seems to be silently dropping sequences from the index.
Working example:
- download circBase hg19 circRNA sequences.
- count them (140790)
- index them and count ag…
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Hi, I would like to clarify something about STAR. I understand that it takes the RNAseq data reads, and align them based on an annotation file. Because it is a splice aware program, it can also recogn…
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It seems the Chimeric.out.junction file from STAR chimeric alignment would output the internal junction information. We could use that information to analysis the internal splicing pattern of circRNAs…
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Hello,
kallisto (0.44.0) seems to be silently dropping sequences from the index.
Working example:
- download [circBase hg19 circRNA sequences](http://www.circbase.org/download/human_hg19_cir…
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I have finsh my circRNA work with CIRI_v2.0.6, and get nearly 20000 circRNAs from each sample. Then i start my work with find_circ2，but i got no results at the last step. I don't the reason.
This i…
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Dear Dieterich-lab,
I'm having some issues running DCC (version 0.4.7) which I hope you can help me with.
I'm trying to run the software in a virtual environment on python version 2.7.15rc1
…
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Hi Tobias,
I am attempting to run DCC on my data but the program does not pass the 'Filtering by read counts' step. I have the most recent version from GitHub installed.
Here is the log file fr…