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I have noticed some splice junction output that does not make any sense (i.e. no supporting reads)
in /prj/circRNA_ENCODE3/workflow/DCC_CD_07_2017/CircSkipJunctions
I found
`1 26255171 …
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DCC version 0.4.4
GENCODE v27 annotation for GRCh38
STAR 2.5.3a indexed GRCh38 with GENCODE v27 annotation
I run DCC after mapping the stranded paired-end ribodepleted RNAseq data in the three p…
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How are single exon genes / circRNAs treated when computing the enrichment in contrast to the linear genes?
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In addition to the overview plots, a "Top 10" plots with one plot per circRNA/RBP would be helpful.
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DCC crashes when using the following command line:
```
DCC @samplesheet -mt1 @mate1 -mt2 @mate2 -T 8 -D -N -an
/data/yaoyh/circRNA/GTF_file/gencode.v26.annotation.gtf -Pi -F -fg -G -A
/data/yaoyh/…
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MP GO:0000964 mitochondrial RNA 5'-end processing
please add parent GO:0000963 mitochondrial RNA processing
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Hi,
I have been trying to run KNIFE v1.4 on some of our RNAseq data. For this dataset we did some UMI based dup marking on the bams and re-converted the dup marked bam to fastq in order to run KNIF…
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Hi,
I am trying to run KNIFE_v1.4 on some of our samples and am running into a few errors for some of them. I am getting these during the call to predictJunctions_tableData.r
**Error 1:**
Err…
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Hi,
I am running into the attached error when running DCC where it says it cannot find the bam index or that the bam is not sorted by coordinate, but both conditions are true for my dataset.
[…
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When run in feature mode, in order to compute the peaks / length the length is taken from the annotation.
This behavior will cause problems when the circRNA is located in an exon-rich region of th…