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Hi Dieterich-lab,
Just a quick question - Are the Chimeric.Junction.out counts in the LinearCount file the raw counts for the host-mRNA at the location of the circExons? I.e. if you have a 2-exon c…
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I have been trying to follow the DCC & FUCHs pipeline but am encountering errors with the FUCH stage.
I aligned my reads as described in the DCC https://github.com/dieterich-lab/DCC and circtools …
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Hi, I have a question about the circRNAs with close position. in the paper you said: CircRNA reads passing these filters are then merged if junction ends are very close.
while in the code,is this scr…
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Hi, I'm having trouble getting this to run with our data which is stranded paired end 150bp Illumina data with ribosome depleted totalRNA from several rat tissues. I've performed the alignment both …
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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 wonder if at any stage during annotation you filter out mitochondrial back splice junctions? When I parse the alignment, there are some back splices listed in the back_splice_junction.bed, but when …
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Hi,
As, I successfully installed CircMarker; and when I tested it on my one sample I am getting the error like this
The first vChrom Size: 25
*** Error in `./CircRnaDetectDraft': double free or c…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/selcenari/ceRNAnetsim
Confirm the following by ed…
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Hello,
I receive the following error when attempting to run the Primer Design module:
Command:
`circtools primex -d /DCC/CircCoordinates -g gencode.v26.primary_assembly.annotation.gtf -f G…
udube updated
5 years ago
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When I am running Circtools with detect module everything goes smoothly but suddenly it stops everytime with same error
Do you have SJ.out.tab files in your sample folder? DCC cannot find it.
This t…