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* spladder version: 2.2.1
* Python version: 3.5.2
* Operating System: Ubuntu 14.04
### Description
I've had trouble finding "ground truth" test cases of clear splice alterations that I can tes…
jfass updated
2 years ago
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Hi Alex,
Not really an issue, but rather a question - is there a chance to pass 3 fastq files to STARsolo to analyze 2 paired end reads and 1 cellBC+UMI?
Thanks ahead!
Cheers,
G
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Hi!
Thank you for this excellent package. I am using TEcount to quantify gene and TE expression in mouse samples. I obtained the TE gtf file (GRCm38_GENCODE_rmsk_TE.gtf) from http://hammelllab.labs…
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Example: https://mila.quebec/en/publications/
It would be nice to reuse the same code as in the Mila website. Not sure if that's 'easily' possible via RTD
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Hi Alex,
I am currently using STARsolo on a Smartseq2 dataset of isolated nuclei and would like to include intronic reads in counting. When comparing `Gene` and `GeneFull` counts from the same run …
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Hi Sean, @seandavi
I am getting an error in both release and devel using the `gdcdata` download function.
Was there a change to the API with accessing legacy archive data? :thinking:
``` r
l…
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Hi,
I use StringTie2 to assemble rna from samples in 2 conditions, with 3 replicates in each condition.
I end up with a gtf file like this one for each sample:
![image](https://user-images.github…
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Hi,
I was wondering if there is a tabular info of the relation between splicing in/out sites and exons of genes. It will be very helpful when the gene is very long. Thanks
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Currently the variant peptides with fusion are labeled as `FUSION-:-:`, which causes a problem to `filterFasta`. In `filterFasta` we take a gene expression table, which has the abundance of each trans…
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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…