User: feng920308

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feng9203080
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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 feng9203080
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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 feng9203080
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Comment: C: Correlation in RNAseq
... Thanks a lot for your great help! ...
written 3 months ago by feng9203080
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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 feng9203080
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Correlation in RNAseq
... 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 ...
correlation rna-seq written 3 months ago by feng9203080 • updated 3 months ago by Carlo Yague5.7k
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How to set the motif length in MEME.
... 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. ...
chip-seq meme motif written 6 months ago by feng9203080 • updated 6 months ago by JC12k
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Is trim data to borders still necessary for ChIPseq.
... 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 ...
chip-seq written 6 months ago by feng9203080
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Comment: C: How to normalize ChIPseq and RNAseq. Especially for bam file.
... Thank you very much! ...
written 6 months ago by feng9203080
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How to normalize ChIPseq and RNAseq. Especially for bam file.
... 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 ...
chip-seq bigwig rna-seq bw written 6 months ago by feng9203080 • updated 6 months ago by ATpoint46k

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