User: feng920308
feng920308 • 0
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Posts by feng920308
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Comment:
C: Correlation in RNAseq
... Thanks a lot for your great help! ...
written 3 months ago by
feng920308 • 0
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Comment:
C: Correlation in RNAseq
... Thanks a lot for your suggestions.
I agree that it is better to use the read counts per gene rather than mRNA abundance to calculate the Pearson correlation.
However, I am trying to reproduce a paper (https://doi.org/10.1016/j.molp.2018.01.008), in which I found that they analyze the Pearson correl ...
written 3 months ago by
feng920308 • 0
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Comment:
C: Correlation in RNAseq
... Thanks a lot for your great help! ...
written 3 months ago by
feng920308 • 0
0
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2
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222
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Comment:
C: Correlation in RNAseq
... Sorry for your confusion. I want to correlation the location of modification sites of nucleotide in mRNA from different samples. ...
written 3 months ago by
feng920308 • 0
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... How to analyze the Pearson correlation coefficient of mRNA abundance between two biological replicates?
Can I use deeptools?
How to analyze the Pearson correlation coefficient of modification sites of nucleotide in mRNA?
I have already got the modification sites, but I do not know how to analyze the ...
written 3 months ago by
feng920308 • 0
• updated
3 months ago by
Carlo Yague ♦ 5.7k
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... I used meme-chip command to find my motif in the ChIPseq data.
However, my results had 25 bp. The paper shows that the motif had only 18 bp. Therefore, I want to know which command I can use to set the length of the motif in meme-chip. ...
written 6 months ago by
feng920308 • 0
• updated
6 months ago by
JC ♦ 12k
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... The "Biostar-handbook" says trim data to borders is good.
***"As we mentioned this before ChIP-Seq data in general and ChIP-Exo in particular measures the left-right borders of the binding sites rather than the center of them. Even though tools should be able to reconstruct these borders algorithm ...
written 6 months ago by
feng920308 • 0
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... Thank you very much! ...
written 6 months ago by
feng920308 • 0
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... Recently, I have read "Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5 0 Promoters in Yeast". However, I did not understand how they did the normalization for the ChIPseq and RNAseq.
***For ChIPseq***
"Gcn4 occupancy profiles were obtained from the alignment (.bam) files using th ...
written 6 months ago by
feng920308 • 0
• updated
6 months ago by
ATpoint ♦ 46k
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