User: morteza.khabiri

Reputation:
10
Status:
New User
Location:
USA/Ann Arbor/Biological Chemistry
Website:
http://freddolino-lab....
Last seen:
1 month, 1 week ago
Joined:
1 year, 6 months ago
Email:
m**************@gmail.com

Postdoc in the Freddolino's lab. I am working on mapping of genetic regulatory networks of large nucleotide dataset

Posts by morteza.khabiri

<prev • 21 results • page 1 of 3 • next >
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Comment: A: How to visualize Hi-C bed file format?
... Practically there is two files one is "bin" which looks like: cbin chr from.coord to.coord count 1 2L 5000 10000 16 2 2L 10000 15000 34 3 2L 15000 20000 11 4 2L 20000 25000 15 ...
written 7 weeks ago by morteza.khabiri10 • updated 7 weeks ago by genomax57k
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How to visualize Hi-C bed file format?
... Hi All, There is a bed format file for Hi-C data form a supplement of a paper which I would like to visualize it. Is there any software or way that I can use to visualize it? I hope I don't need to do the raw data analysis? Thanks, ...
genome hi-c written 7 weeks ago by morteza.khabiri10
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How to study open promoters are correlated with high expression using MNase and RNA-seq data?
... Hi all, I have two sets of data, one from MNase and the other from RNA-Seq data. Both experiments were done in the same condition. I want to see whether open promoters are correlated with high expression. How can I do this analysis? Any idea is appreciated. Thanks, ...
mnase rna-seq written 8 weeks ago by morteza.khabiri10 • updated 10 days ago by Biostar ♦♦ 20
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Comment: A: PCA plot for TOP 500 genes + prcomp
... pcaExplorer is a cool package which can do it. You can find more information here: [pcaExplorer][1] [1]: https://rdrr.io/bioc/pcaExplorer/f/vignettes/pcaExplorer.Rmd ...
written 8 weeks ago by morteza.khabiri10 • updated 8 weeks ago by genomax57k
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PCA plot for TOP 500 genes + prcomp
... Hi all, Do you know how do I plot PCA for top500 genes by prcomp() the same as PCAplot in Desq2? I would like to plot the PCA for top 500 genes for PCA3 and PCA4. Thanks ...
rna-seq written 8 weeks ago by morteza.khabiri10
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Answer: A: How to get PCA3 and PCA4 from Deseq2?
... Thanks, everyone. For those who are interested in plotting the PCA component 3, 4 and ... the following lines could help too. library("DESeq2") library(ggfortify) project.pca <- prcomp(t(assay(dds)[select,])) pdf("PCA34.pdf") autoplot(prcomp(t(assay(dds)[select ...
written 8 weeks ago by morteza.khabiri10
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How to get PCA3 and PCA4 from Deseq2?
... Hi All, I am plotting PCA via pcaplot in Deseq2. I am interested to look at other pca plots like pca3 vs. pca4 as well. How could I have this information in Deseq2? Thanks, ...
rna-seq written 9 weeks ago by morteza.khabiri10
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(Closed) ChIA-PET with two antibodies
... Hi All, Is it possible to do ChIA-PET exp. with two different Antibodies at two steps? Imagine we have a complex with two proteins, proteinA and proteinB. Each of these proteins can interact with many different places in the genome but the complex of the proteinA and B will interact to fewer places ...
chromatine remodeling chiia-pet written 10 weeks ago by morteza.khabiri10
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Answer: A: massive pairwise sequence alignment
... I am answering my question, since It may help people with similar problem. The fast massive alignment is possible by applying Bowie. When you do alignment using Bowtie2 it will tell you how many sequences are repeated. And you can delete the repetitive sequences by extracting it from sam file (Bowti ...
written 8 months ago by morteza.khabiri10
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Comment: C: Split RNA-seq reads
... cutadapt -u 5 is also do the same job!!! ...
written 8 months ago by morteza.khabiri10

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