User: Barry Digby

gravatar for Barry Digby
Barry Digby310
Reputation:
310
Status:
Trusted
Location:
National University of Ireland, Galway
Twitter:
@BarryDigby
Last seen:
15 hours ago
Joined:
1 year, 10 months ago
Email:
b********@hotmail.com

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Posts by Barry Digby

<prev • 62 results • page 1 of 7 • next >
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Comment: C: can I use some interesting genes(such as a subset of DEGs from RNA-seq result) t
... You can, but perhaps should not. You are deliberately omitting results from the experiment, and run the risk of spurious results depending on the size of the subset. You are better off doing a literature search on the subset of genes. (I mean you chose them for a reason, right?). ...
written 6 days ago by Barry Digby310
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Comment: C: Editing tools script in a docker container
... I managed to do what I set out to do in the answer below, not sure if it is useful though. My scripts are being run by nextflow, using containers for processes. Inspecting the `.nextflow.log` file, I've run into **"[Errno 28] No space left on device:"** errors which kill the nextflow process, and ...
written 24 days ago by Barry Digby310
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Answer: A: Editing source scripts in a container
... Ok here goes. The motivation for this was to specify where CIRIquant writes its temporary SAM | BAM files. I ran into disk space issues on my local cluster so wanted to specify a `"/scratch"` dir. All I had to do was edit the wrapper scripts that execute CIRIquant. # Pull image to edit Pull ima ...
written 25 days ago by Barry Digby310
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Editing tools script in a docker container
... Hi, I have created a container using singularity, pulling an image from docker hub ([here][1]). All i want to do is add a `-T /data/scratch/` flag to samtools sort commands in two of the tools wrapper scripts. I have run `sudo singularity shell xxx.simg` and viewed the scripts, which are all `-r ...
dockerhub singularity docker written 25 days ago by Barry Digby310
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Answer: A: In need of guidance: RNA-seq analysis
... Hi Jonathan, 1. GSEA is a form of pathway analysis.. depends how far you want to go. Here is an example of how to use fgsea (fastGSEA) here by Stephen Turner [https://stephenturner.github.io/deseq-to-fgsea/#using_the_fgsea_package.][1]. For human data, I download gene set files (.gmt) [here][2], n ...
written 7 weeks ago by Barry Digby310
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Comment: C: How to perform iteration task inside a docker image (RNA-seq analysis)
... No problem. Let me know if you run into trouble :) ...
written 8 weeks ago by Barry Digby310
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Answer: A: How to perform iteration task inside a docker image (RNA-seq analysis)
... I would highly recommend using [nextflow](https://www.nextflow.io/docs/latest/index.html) or some other workflow manager as they are designed precisely for the task you are describing. You can write a simple script to read in the bam files, and execute the cufflinks command. Using the [-with-docke ...
written 8 weeks ago by Barry Digby310
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Answer: A: How to take input TCGA miRNA data in Limma R package for differential expression
... Sorry for deleting/re-posting answer. Original answer had a fatal flaw.. So, here is a script that will take the `read_counts` data that Kevin is referring to from each file in the directory, and make a counts matrix for you. The first column will be the `miRNA_ID` and each column name will be the ...
written 9 weeks ago by Barry Digby310
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Comment: C: Missing gene symbols in bustools output
... I think I may not have been very clear. I am referring specifically to the genes.txt output from `bustools count`. In the second link you provided me, the dataset has a `genes.tsv` file, that has both ENSG ID + symbols. In my own attempts using `bustools count`, my output has only ENSG ID. This make ...
written 9 weeks ago by Barry Digby310
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Comment: C: Missing gene symbols in bustools output
... Thanks for the response Páll. I'll integrate the `py` script into my nextflow script and hopefully get to the bottom of this over the weekend. I've noticed the ensembl GTF file uses version Id's but the ensembl cDNA file does not. Annoying discrepancy. Anyway I'll get to work and post a solution ...
written 10 weeks ago by Barry Digby310

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Student 5 weeks ago, asked a question with at least 3 up-votes. For Counting Gene Clusters from Antismash Output
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