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`python2.7 /root/software/RNASeq-MATS.py -b1 cat b11.txt-b2cat b22.txt -gtf /root/software/gtf/hg38.knownGene.gtf -o out_test -t single -len 100 -a 8 -r1 72,75 -sd1 40,35 -r2 70,65 -sd2 48,45 8 -c 0.0…
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I am trying to process RNAseq data and getting the below error,
```
Reading file /superFreq.analysis/VarscanVariants/08_1-205.sorted.vcf...done.
Processing data...Error in `[ vcfToPositions -> […
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Updating this ticket with the latest histologies:
There are some minor issues with the merged histologies file that we can discuss in the next toolkit meeting. Using the latest merged histologies f…
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Hello,
I am testing alevin-fry on some public sc-RNAseq data (GEO accession: GSE81076). The issue that I have is that when I process the gene count x cell matrix in R and perform per-cell metrics,…
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#### What analysis module should be updated and why?
The `tumor-gtex-plots` module should be updated to subset each-cohort independent primary tumor RNA-seq samples before generating plots/resu…
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**Is your feature request related to a problem? Please describe.**
As there are new data types, we need a better way of tracking what is available, and who/when it has been analyzed.
**Describe t…
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Possibly we need to update the link for the RNA-Seq workflow, per below.
Might want to be explicit which workflow file this was? I seem to remember (?) we used a deprecated one: https://github.com/…
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Thank you for sharing your code!
I am taking the snakemake pipeline for a spin, and it is not obvious what the "assembly/{refgenome}_full.fa" supposed to be. From scanning the code briefly, I thoug…
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Dear Gviz authors,
I have been working on a large locus plot using Gviz and wanted to reduce the number of yTicks to make the plot more comprehensible.
I was able to set the yTicks using `yTi…
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Hi,
I have a problem that is somewhat similar to the ones reported in issue #157 and #115
We run fusioncatcher on a large cohort (> 600 samples) with RNAseq data from leukemic bone marrow.
In so…