User: Anthony.Knox

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Anthony.Knox50
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Posts by Anthony.Knox

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Comment: C: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via K
... What is the reference genome that you use for this dataset? I tried Kallisto alignment with both Human GRCh37 and GRCh38 (from Ensembl cDNA) and I am getting read counts of 0 for all transcripts. ...
written 10 months ago by Anthony.Knox50
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Comment: C: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via K
... Thank you for the reference! ...
written 10 months ago by Anthony.Knox50
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Comment: C: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via K
... Thank you very much for the suggestion - I was looking for a dataset that would be quicker to download for demonstration purposes. I am running through the program with this dataset right now and will most likely update the ReadMe to include it as a demo. But you are correct, the fastq-dump is the m ...
written 10 months ago by Anthony.Knox50
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Comment: C: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via K
... I completely agree with your stance on pipelines and the necessity for people to really delve into their own specific needs for their own specific project. While I understand that the downside of strictly following a given pipeline is that you are confined in terms of setting parameters and producin ...
written 10 months ago by Anthony.Knox50
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Tool: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via Kallisto and DESeq2
... Hi All, In short: I developed a program as a GUI to help set up and execute RNA-Sequencing analysis via Kallisto and DESeq2, starting with fastq files, either downloaded with directions from the program, or provided by the user. The program provides customized Bash and R scripts to automate the pro ...
deseq2 kallisto rna-seq tool written 10 months ago by Anthony.Knox50 • updated 10 months ago by Charles Warden7.4k
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Answer: A: SRA Toolkit Prefetch error when downloading dbGaP SRR files
... For anyone interested, it turns out that this is a bug where prefetch is leaking file descriptors. As a current workaround (for 2.8.2), just use this command before calling prefetch: ulimit -n 10000 This will set the maximum number of open file descriptors to 10000 (mine was at 256 as a defaul ...
written 23 months ago by Anthony.Knox50
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SRA Toolkit Prefetch error when downloading dbGaP SRR files
... I am trying to download SRR files that requires authorization through dbGaP, so I have to download it through command line. I downloaded the Aspera Connect CLI as well as the Aspera Connect app and imported the repository key file correctly. I am using prefetch-2.8.2. I am reading in a text file wit ...
ncbi prefetch sra toolkit dbgap rna-seq written 23 months ago by Anthony.Knox50
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DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
... I am relatively new to this type of analysis, so bear with me but when I am following the Analyzing RNA-seq data with DESeq2 (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) I get an error when creating a heatmap. I know this issue has been addressed [here][1], but ...
pheatmap deseq2 rna-seq gpar written 2.0 years ago by Anthony.Knox50

Latest awards to Anthony.Knox

Scholar 23 months ago, created an answer that has been accepted. For A: SRA Toolkit Prefetch error when downloading dbGaP SRR files

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