User: dcheng1

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dcheng10
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Posts by dcheng1

<prev • 28 results • page 1 of 3 • next >
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Which tool is most popular for GO over-representation analysis?
... I noticed GO consortium use PANTHER on their website. So it looks like PANTHER is a very official tool. I'm wondering why not everyone using it. Is there a reason for not using PANTHER? ...
chip-seq rna-seq written 21 days ago by dcheng10 • updated 17 days ago by Shalu Jhanwar350
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How to generate high-resolution genome track?
... I'm wondering what method used most commonly to generate high-quality genome track? (like the one showed below) I use IGV, but the resolution of the exported image is not very high. https://ibb.co/fMFMgH8 ...
chip-seq rna-seq sequencing written 7 weeks ago by dcheng10 • updated 7 weeks ago by igor11k
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Comment: C: Minimal mapping score of bowtie2
... Thanks for your help! ...
written 10 months ago by dcheng10
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Minimal mapping score of bowtie2
... I'm trying to filter out low-quality alignment before calculating correlation coefficient. What's the cut-off mapping score people usually use to get rid of bad alignment for bowtie2? ...
bowtie2 chip-seq mapping written 10 months ago by dcheng10
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Comment: C: Detect trend among multiple ChIP-seq data
... I thinks I understand the part before heatmap. Assume I have n peaks in the consensus list, and I have m data. Then I will have a n x m matrix. Each value in the matric is the normalized read counts. Then I guess I need to plot a heatmap using the n x m matrix? I don't understand "select the cluster ...
written 11 months ago by dcheng10
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Comment: C: Detect trend among multiple ChIP-seq data
... Thanks for your help! ...
written 11 months ago by dcheng10
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Detect trend among multiple ChIP-seq data
... I want to find loci where peak signal change gradually among multiple ChIP-seq data. For example, in the picture below, peak intensity gradually decrease from the top data to the bottom. I'm wondering if there are any tools can help me find those loci? Any suggestions are greatly appreciated! ![htt ...
chip-seq written 11 months ago by dcheng10 • updated 11 months ago by ATpoint36k
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Comment: C: Calculate ChIP-seq correlation in promoter regions
... I tried spearman correlation, it indeed gives slightly lower correlation than pearson did. Thank a lot!!! ...
written 17 months ago by dcheng10
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Comment: C: Calculate ChIP-seq correlation in promoter regions
... Hi Devon, thanks for your helps! I have a follow-up question: suppose a bin contains no reads or few background noise reads in both replicates, then the correlation between the two replicates in this bin will be almost 1. But obviously this is not the perfect correlation we want, and the correlation ...
written 17 months ago by dcheng10
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Calculate ChIP-seq correlation in promoter regions
... I read a few papers that calculate Pearson correlation coefficient of ChIP-seq replicates **in promoter regions**. However, even for active marks like H3K4me3, not 100% of peaks are located within promoter regions. **Would it be more accurate to calculate the correlation using the bed file from MA ...
chip-seq sequencing written 17 months ago by dcheng10 • updated 17 months ago by Devon Ryan96k

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Popular Question 17 months ago, created a question with more than 1,000 views. For how to find the primer for the promoter of VEGF gene?
Popular Question 22 months ago, created a question with more than 1,000 views. For how to find the primer for the promoter of VEGF gene?

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