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Hello! I have already created a annot.list, and as far as I understand, if I have 4 samples for my experiment, this is what I do:
```
cdata
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This link is broken:
Users can download them from our FTP (ftp://treeslab1.genomics.sinica.edu.tw/treeslabtools/circRNA_ASD).
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To enable STAR's chimeric output files to work with [STAR-Fusion](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1842-9), the option `--chimOutJunctionFormat 1` is used. Loading s…
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Hi,
I have installed CircMiner 0.2b on Ubuntu.
There was no problem with indexing. I was able to get the index files as below for indexing GRCm38.primary_assembly.genome.fa:
GRCm38.primary_as…
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Hi,
I have been using circRNAprofiler to perform downstream analysis on output data from CIRCExplorer2.
I have been able to work with the full pipeline as showed on [Bioconductor](https://www.bi…
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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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Hi everyone,
I am beginner in Linux and I am trying to do mapping step to identify circRNA in my RNA_seq libraries.
Here what I have done for it:
_ bowtie2-build Gmax_275_v2.0.fa Gmax_indexed
_bo…
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I found lots of start and end points are different from the original database. For example, hsa_circ_00001 has 230350957-230357321, but the database indicates 230486703-230493067 with a shift. There a…
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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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All circRNAs were labeled as "intergenic" when using GTF downloaded from UCSC table browser