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1) add a tool to verify strandedness for RNAseq:
https://github.com/betsig/how_are_we_stranded_here
2) Add gene/transcript expression comparison/correlation between stringtie and kallisto
3) ut…
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I followed QoRTs "Example Walkthrough" to run JunctionSeq and got the results. However,
I noticed the number of aggregate genes in GFF vs allGenesresults file are different.
GFF file:
`grep -c…
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Hello,
I noticed that gene_quanti seems to be using a strangely high amount of memory.
The command I'm running is: `reademption gene_quanti -p 4 --features 'gene,cds,region,exon' --project_path …
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Hey there,
It seems to me that due to how most RNAseq libraries are now constructed, most people who want to count reads per feature with summarizeOverlaps will actually want to use `ignore.strand …
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I want to download all the clinical data from the rnaseq data selected:
```
expands = c("diagnoses","annotations",
"demographic","exposures")
clinResults = cases() %>%
Genomic…
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We need to dynamically create a dependency graph based on the input and output files to visualize the progress of the workflows.
Some options we should consider from snakemake
--d3dag, --dag, --ru…
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```
What steps will reproduce the problem?
1. mapping 50 bp single end illumina reads to bacterial genome
2.
3.
What is the expected output? What do you see instead?
reported mapped # of reads does n…
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Hello. Thank you for creating this tool. I'm trying to use clipper in my local computer but haven't been able to install it. I downloaded the yml file, but when I run the `conda env create -f environm…
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I installed R-3.4.1 by Miniconda, and managed to installed the GDCRNATools, but while testing with your instruction to download RNA data (http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNAT…
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I have downloaded SARC RNA-seq data by HTseq-Count workflow type through TCGAbiolinks. But I need SARC RNA-seq data based on Transcripts Per Million (TPM) value. Can TCGAbiolinks help me to download T…