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@iskandr is changing a few things around. Also, his comment from before:
> My only suggestion would be to maybe increase the minimum MAPQ to 1 and if you're ultimately using the counts of neoepitopes…
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Brilliant package and super easy to use!
I am trying to add some custom transgenes (TagBFP2,EGFP, TdTomato, etc.) as I have successfully done in the past with CellRanger and StarSolo but I can't se…
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Hi!
i noticed that `SelectGenes` Available genome are: hg19, hg38, mm9, and mm10
can i use the genomes of other species?
If so, how exactly should I do it
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> devtools::install_github("shouguog/cellcallEXT")
Downloading GitHub repo shouguog/cellcallEXT@HEAD
Skipping 1 packages not available: ComplexHeatmap
── R CMD build ───────────────────────────────…
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I cannot run rMats the normal way so I have run it from a singularity I pulled from [here](https://hub.docker.com/r/mcfonsecalab/rmats). The following variable and command is what I used:
The varia…
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```
What steps will reproduce the problem?
1. read PSL data
2. write KISS
3. note BLOCK_TYPES
What is the expected output? What do you see instead?
We should have exon type blocks and intron type bl…
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Great app, thanks!
Why can't we push aside a sequence by just pushing the first amino-acid or nucleotide from the sequence? When sequences are long, this would be easier for local alignments. And, I …
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we assumed that we weren't able to use the GFF3 file for indexing or featurecount so we needed to convert it to GTF format.
we first used genometools "gt gff3_to_gtf our_gff_file > new_gtf_file and t…
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When working on complicated genes, which require iterative blasting or blasting for specific exons or motifs individually, the back browser functionality of the legacy system recalls the species and t…
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## Feature request
### Tool(s) or class(es) involved
_Funcotator_
### Description
Need to add more indel test cases for HG38 for completeness.
The set of test cases should be:
{3' and…