User: dganiewich

gravatar for dganiewich
dganiewich90
Reputation:
90
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Trusted
Location:
Buenos Aires, Argentina
Last seen:
2 months ago
Joined:
11 months ago
Email:
d*********@leloir.org.ar

Posts by dganiewich

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Update below, even Batch Effect removal was not enough ...
written 3 months ago by dganiewich90
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Answer: A: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... For anyone that encounters a similar situation: Even after batch effect removal, the library method is so different that it was not possible to compare them after all. QC plots showed that samples still clustered by library method and separated from their own same origin sample. This paper helped ...
written 3 months ago by dganiewich90
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Thank you for your comment skbrimer! ...
written 4 months ago by dganiewich90
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Great point. It is indeed for mRNA. Thanks ...
written 4 months ago by dganiewich90
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Thank you kristoffer! I will definitely use this! ...
written 4 months ago by dganiewich90
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Can I perform differential gene expression with samples from Poly-A and Ribo-deplation ?
... Hi, I have a question regarding differential gene expression analysis when the samples library method is different. I have 10 samples total, 3 from one condition and 7 from the other. Among the first 3, 2 where sequenced using poly-a and one with ribo depletion library preparation method. In the ...
rna-seq differential expression written 4 months ago by dganiewich90
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Comment: C: CWL docker command user
... I just realized that you use the Github file and not the Docker image, maybe that is what I am doing wrong... I'll check and get back to you ! ...
written 6 months ago by dganiewich90
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Comment: C: CWL docker command user
... Hi Tom, thank you very much for your help! Indeed, I have stuggled a lot with bioinformatic stuff !! I'm sorry for my belated response, but I have yet not been able to make it work... Maybe there is something wrong with my importation of the dockerfile? Just to be sure, my new code has: #!/us ...
written 6 months ago by dganiewich90
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Comment: C: CWL docker command user
... Hi Tom! Sorry for the belated response. Here is the command line tool where you can see the docker container: #!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool baseCommand: - "gatk" - "MarkDuplicatesSpark" hints: DockerRequirem ...
written 6 months ago by dganiewich90
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CWL docker command user
... Hi! I am using CWL to run a program, and when I do cwl-runner tool.cwl tool_params.yml, the docker command has a --user=500:500 When I try running my tool, there is an id error that doesn't allow me to run it correctly (see https://gatkforums.broadinstitute.org/gatk/discussion/comment/59004#Comme ...
cwl-runner cwl docker written 6 months ago by dganiewich90 • updated 6 months ago by Tom520

Latest awards to dganiewich

Scholar 6 months ago, created an answer that has been accepted. For A: GATK4 Mutect2 variants IDs not shown
Scholar 8 months ago, created an answer that has been accepted. For A: GATK4 Mutect2 variants IDs not shown

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