User: nickhir

gravatar for nickhir
nickhir10
Reputation:
10
Status:
New User
Location:
german research cancer center (DKFZ)
Last seen:
6 hours ago
Joined:
3 weeks, 4 days ago
Email:
h*****************@gmail.com

Posts by nickhir

<prev • 9 results • page 1 of 1 • next >
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Questions regarding whole exome sequencing
... Hey everybody, I am currently informing myself about Whole exome sequencing (WES) and there are a couple of things that still confuse me: 1) I read that WES "does not permit deep sequencing". Can somebody elaborate why this is the case? 2) I checked this [website][1] to get an idea about coverage ...
wes sequencing written 1 day ago by nickhir10 • updated 23 hours ago by Kevin Blighe59k
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Comment: C: How to performe differential gene expression analysis for a single patient
... That makes a lot of sense, thank you! Do you know if the *lfcshrink* function of DESeq2 works without replicates? Because I think this would also help in determining "significantly" differentially expressed genes. ...
written 3 days ago by nickhir10
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Comment: C: How to performe differential gene expression analysis for a single patient
... Thank you for your answer! Could you maybe elaborate what you mean with *minimal trusted value*? I have never heard of it in the context of DGE analysis ...
written 4 days ago by nickhir10
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How to performe differential gene expression analysis for a single patient
... Hey everybody, I think this is a basic question, but somehow I am really confused right now and it would be amazing if somebody could point me the right way. I was wondering how it is possible to perform DGE for a single cancer patient. I thought, that if you use programs like DESeq2, you need bi ...
rna-seq dge written 4 days ago by nickhir10
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Comment: C: Ensembl gene ID meaning of the underscore
... Perfect! Thank you very much for pointing that out and taking the time to answer! ...
written 10 days ago by nickhir10
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Comment: C: Ensembl gene ID meaning of the underscore
... Do you have nonetheless an idea what it could mean? I am surprised that there is no info about this in the internet. Like I said I just downloaded the GTF and genome FASTA from https://www.gencodegenes.org/human/release_33lift37.html , which is widely used to my knowledge. Do you think the GTF file ...
written 11 days ago by nickhir10
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Ensembl gene ID meaning of the underscore
... Hello everybody, I performed a DGE analysis and now I am trying to convert the gene ID to gene names. The problem is that virtually all of my gene IDs look somewhat like this: ``ENSG00000000003.15_4``. In the list of gene IDs which correspond to the gene name, the gene IDs have this format: ``ENSG ...
ensembl geneid written 12 days ago by nickhir10 • updated 11 days ago by Ben_Ensembl1.4k
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GNU Parallel Number of Possible Threads
... Hello everybody, I think I have a fairly basic question. I just discovered the GNU parallel package and I think my workflow can really benefit from it! I am using a loop which loops through my read files and generates the desired output. The command that is excecuted for each read looks something ...
multithreading parallel gnu rna-seq star written 20 days ago by nickhir10 • updated 20 days ago by ATpoint34k
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How to evaluate the performance of an RNA-seq pipeline
... Hello everybody, I am fairly new to the RNA-seq workflow and I am currently struggling how to evaluate the performance of the RNA-seq pipeline I am trying to establish, which will be used to investigate differential gene expression. Lets say I have 3 different pipelines: 1. kallisto -> tx ...
R differentialexpression deseq2 rna-seq written 25 days ago by nickhir10 • updated 25 days ago by geek_y11k

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