User: aropri

gravatar for aropri
aropri50
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7 months ago
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a*****@albany.edu

Posts by aropri

<prev • 58 results • page 2 of 6 • next >
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Comment: C: Use bedtools intersect to see how much coverage you had of a specific coordinate
... I would like to post my input so you can check, where do you suggest I upload it so you can see. I would have replied earlier but because I have a new account can only post so much in 5 hrs so couldnt reply. ...
written 7 days ago by aropri50
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Comment: C: Use bedtools intersect to see how much coverage you had of a specific coordinate
... chr12 75943973 75954960 0 10987 0.999909 What do the last 3 columns represent ...
written 7 days ago by aropri50 • updated 7 days ago by genomax92k
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Comment: C: Use bedtools intersect to see how much coverage you had of a specific coordinate
... chr12 75943973 75954960 0 10987 0.999909 This is the output I got when for one of my regions when I ran this, what are the last 3 columns representing, a little confused there. Appreciate your help. ...
written 7 days ago by aropri50
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Comment: C: Use bedtools intersect to see how much coverage you had of a specific coordinate
... Thanks, this is helpful, going to try out the couple of ways you guys suggested ...
written 7 days ago by aropri50
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Comment: C: Use bedtools intersect to see how much coverage you had of a specific coordinate
... Thank you, will try this out and see how it goes. ...
written 7 days ago by aropri50
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Use bedtools intersect to see how much coverage you had of a specific coordinate
... How would I compare a bed file and a bam file using bedtools intersect to see how much coverage I had of specific coordinates in my bed file? Thank you in advance for your help! ...
chip-seq written 7 days ago by aropri50 • updated 5 days ago by Alex Reynolds31k
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Comment: C: Collapse two or thee bed files into one bed file using bedtools merge
... Thank you so much. This is what I was looking for and appreciate your quick response. I did try looking at the documentation of the bedtools merge but was a little confused. Thanks again! ...
written 7 days ago by aropri50
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Collapse two or thee bed files into one bed file using bedtools merge
... I have a 4 bed files of peak coordinates from ChIP seq, I was wondering is there a way to collapse them into one bed file where all the peak coordinates are now in one bed file from the 4 different files using bedtools merge. And if there is a way what would the command look like. Appreciate any hel ...
chip-seq written 7 days ago by aropri50 • updated 7 days ago by ATpoint41k
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Comment: C: Compare Super Enhancers in normal vs breast cancer cells
... I want to compare peaks and I think I can do that by collapse A.SE.bed and B.SE.bed into AllSEs.bed using bedtools merge. Quantify coverage of All SEs.bed using A.bam and B.bam and bedtools intersect. Normalize the read coverage to the sequencing depth, and calculate the fold-change between them. Th ...
written 9 days ago by aropri50
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Comment: C: Compare Super Enhancers in normal vs breast cancer cells
... I want to compare the signal of the super enhancer regions that were classified by ROSE in normal and breast cancer cells and see calculate fold change of those regions to see if they are increasing or decreasing in intensity. I have a bed files of super enhancer regions for normal cells (MCF10A) an ...
written 9 days ago by aropri50

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Scholar 6 months ago, created an answer that has been accepted. For A: ChIP seq: Trying to use ChIPQC to measure quality of reads

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