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I'm wondering if there is concise documentation somewhere for reproducing the exact analysis of the TCGA/GTEX data in this [paper](https://www.nature.com/articles/nbt.3772) (but with new samples).
h…
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- https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq
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Understand and identity the workflow of the vartable program.
Which part of the program depends on DNA-data and till where does this dependency continues.
- [ ] How to adjust vartable.py
- [ ] H…
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### Description of feature
A genome note provides meta data related to the specimen used to produce the genome assembly, the specimen used to generate HiC data and the specimen used to produce RNA-Se…
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### Description of feature
The current rna-seq pipeline, generates two bigwig files one each for each strand. it would be great if like chipseq pipeline, it generate only one bigwig files, would be h…
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- https://github.com/ENCODE-DCC/rna-seq-pipeline
- https://www.genome.gov/sites/default/files/Multimedia/Slides/ENCODE2016-ResearchAppsUsers/ENCODE2016_strattan_slides.pdf
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Determine the requirements and potential options for the basis of the Pangenome Annotation RNA-seq pipeline.
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1. Blue color update in theme as used in GenPipes branding / other collaterals. (Update via @pphector the logo for genpipes uses the following blue RBG code: 11-45.9-73.7 or in HTML notation: 1c75bc).…
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# Update May 28th
Today, I was able to complete the pipeline up till deseq2 or possibly featurecounts. The Star script is finished, and now, within the Star rule, I am using samtools to separate th…
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This was reported by one of the users during Seattle Workshop.
Data analyzed with Cufflinks in particular were reported to be susceptible to batch effects. The tuxedo pipeline was replaced in 2016…