User: nickhir
nickhir • 10
- 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
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... 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 ...
written 1 day ago by
nickhir • 10
• updated
23 hours ago by
Kevin Blighe ♦ 59k
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... 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
nickhir • 10
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... 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
nickhir • 10
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... 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 ...
written 4 days ago by
nickhir • 10
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... Perfect!
Thank you very much for pointing that out and taking the time to answer! ...
written 10 days ago by
nickhir • 10
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... 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
nickhir • 10
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... 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 ...
written 12 days ago by
nickhir • 10
• updated
11 days ago by
Ben_Ensembl • 1.4k
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... 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 ...
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... 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 ...
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