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hi guys i try to use hisat2 aligning the fastq file to the index which i have built before, here is the command line:
/home/wyf/miniconda3/bin/hisat2 -x /home/wyf/Pipeline/RNA-seq/02.hisat/Eriochei…
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Dear bcbio community,
In 2011, the Harvard Chan Bioinformatics Core began developing bcbio as an open-source framework to tackle challenges in reproducibility and scalability in the field of next-g…
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See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)
- assembly accession number: GCF_037126465.1
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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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I'm currently working on setting up a simple RNA-seq analysis pipeline using snakemake, and I've integrated the STAR wrapper from snakemake-wrappers. However, I've run into an issue where specifying `…
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RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
http://bioinformatics.oxfordjournals.org/content/30/12/i283.full.pdf+html
Li HD, Menon R, Omenn GS, Guan Y. (2014) The emerging…
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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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It's currently not possible to import an experiment where there are multiple bioassays for the same biomaterial.
The simplest example of this scenario is a dataset with technical replicates where a g…
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Hi, I have read your article “Inference of immune cell composition on the expression profiles of mouse tissue” and I am looking forward to using ImmuCC in my model, but I have RNA-seq data. Here in th…