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So here's one example of the thing I was talking about where you'll look at the sashimi plot for the tumor and see a reported junction and then look at the normal and see a junction that looks essenti…
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-j option will print to stdout, even if -j option is supplied with file name
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Hi.
In most of case, there are both exon and CDS record in gff files.
but there are some CDS regions without exon info in GRCh38.p10 refseq gff files.
```
grep -v partial=true ${tmp_dir}/gen…
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documentation needs to be updated to reflect the additional -j option allowed in cis-splice effects (-j STR Output file containing the aberrant junctions in BED12 format.)
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Hi Stephen!
Thank you for the excellent tool!
I run qorts with
```
java -Xmx10g -jar ~/work/tools/bin/QoRTs.jar QC \
$bam \
ref-transcripts.gff \
${bam}.qorts
```
and in the result ha…
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Hi, I can't get the camel key in the key pattern to work for some reason. I'm using the latest release:
Here is my key pattern:
[auth][year][camel]
Here is my bibtex file:
> % Encoding: …
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Hello, I noticed that the junctions published here:
http://snaptron.cs.jhu.edu/data/srav1/
include only GT/GC/AT donors and AG/AC acceptors.
Is there an explicit filtering at some stage in the pipe…
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Hi,
my vcf file was annotated by VEP(version 84)
and transfrom vep.vcf to maf( TCGA MAF Specification v2.4) file using vcf2maf(latest version)
But during running Genome music0.4 code:
```
genome musi…
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Hi,
I am trying to call fusions in paired end RNAseq data using the following command:
```
tophat2 \
--num-threads=10 \
--output-dir=SKNAS \
--fusion-search \
--no-coverage-search \
--mate…
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Hello, there is no mention of how sQTL analysis is done (which is claimed in the paper). I have completed steps 1 & 2 to get clustered junctions for my dataset and I also have genotypes for these samp…