User: akivab2

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akivab2100
Reputation:
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European Union
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4 months, 3 weeks ago
Joined:
4 years, 11 months ago
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Posts by akivab2

<prev • 17 results • page 1 of 2 • next >
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Batch effect and CCA
... Hi, I saw in a Seurat vignette that when there is a batch effect it is suggested to use CCA instead of PCA. Could someone please explain how and why this works? also, if you could also explain what is the general idea of how we deal with batch effects (what is the logic of solving this issue)? Than ...
cca rna-seq seurat batch effect written 4 months ago by akivab2100 • updated 3 months ago by Biostar ♦♦ 20
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IGV or IGB
... Hi, In the past I used to work with IGB, mainly for DNA-seq. I started working in a new lab, and the genome browser they have been using is IGV. Much of the data viewed in the lab is of RNA-seq and ATAC-seq. I was wondering if there is any preference to IGV or IGB? I found IGB to be easier to use ...
genome browser ngs igb rna-seq igv written 7 months ago by akivab2100 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Tool for categorization of each gene in list according to sub-cellular location
... Thanks, I will check it out ...
written 8 months ago by akivab2100
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Tool for categorization of each gene in list according to sub-cellular location
... Hi, Does anyone know of a tool that accepts as an input a list of different genes and categorize them according to subcellular localization (e.g. which of the genes code to proteins that are found on the cellular surface, which are transcription factors and are in the nucleus, etc.)? Thanks, Akiva ...
genes subcellular rna-seq proteins written 8 months ago by akivab2100
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(Closed) the FPKM in RNA-seq data
... Hey, what is the FPKM value in RNA-seq data? why is it normalized this way and how do i understand the expression levels from it? thanks! ...
fpkm expression rna-seq written 3.9 years ago by akivab2100
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Answer: A: coloring specific mRNA in IGB
... thanks a lot for your help  ...
written 4.1 years ago by akivab2100
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coloring specific mRNA in IGB
... Hi, How do I color specific mRNA from the built in track in IGB version 8.4.0? thanks   ...
mrna igb color written 4.1 years ago by akivab2100
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Comment: A: Bowtie default number of mismatches
... thanks for your help ...
written 4.1 years ago by akivab2100
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Bowtie default number of mismatches
... Hi, Is there a default number of mismatches when not specifying the number of mismatches in Bowtie? Thanks ...
mismatches alignment bowtie written 4.1 years ago by akivab2100 • updated 4.0 years ago by Biostar ♦♦ 20
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Comment: C: Tophat option -p
... thanks for the super quick answer ...
written 4.5 years ago by akivab2100

Latest awards to akivab2

Epic Question 8 months ago, created a question with more than 10,000 views. For the difference between BED files and BedGraph files
Great Question 3.9 years ago, created a question with more than 5,000 views. For the difference between BED files and BedGraph files
Popular Question 3.9 years ago, created a question with more than 1,000 views. For the FPKM in RNA-seq data
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Bowtie default number of mismatches
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Tophat option -p
Popular Question 3.9 years ago, created a question with more than 1,000 views. For what are the control samples when using MACS to find ChiP-seq peaks?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For viewing BED Graph files on the IGB
Popular Question 3.9 years ago, created a question with more than 1,000 views. For the difference between BED files and BedGraph files
Student 3.9 years ago, asked a question with at least 3 up-votes. For the difference between BED files and BedGraph files

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