User: mikysyc2016

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mikysyc201610
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Posts by mikysyc2016

<prev • 90 results • page 1 of 9 • next >
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What is the difference between "findMotifsGenome.pl" and "findMotifs.pl" in homer motif analysis?
... Hi all, Did you try both of them to see what is the difference between these two to do motif analysis with ChIP-seq results? Homer said: Analyzing lists of genes with promoter motif analysis ( findMotifs.pl) Analyzing genomic positions ( findMotifsGenome.pl) After Peakcalling, I want to do motif ...
motf analysis chip-seq written 11 days ago by mikysyc201610 • updated 11 days ago by reskejak10
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Comment: C: A question about "Call differential binding events"
... I did two TF ChIP-seq. And both of them express in same tissue. I want to t compare their binding sites( overlapped and specific). ...
written 5 weeks ago by mikysyc201610
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Comment: C: A question about "Call differential binding events"
... Hi, I use homer to do the process and also use its merge peak parameter. I use IGV to see the specific and overlap peaks, as you mentioned, I think some of the specific peak is real weak( some look like real), do not look like real peak for me. Do you have any suggestion about how to choose the real ...
written 5 weeks ago by mikysyc201610
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total reads for ChIP-seq and RNA-seq
... Hi all, When you know the counts number for each gene(RNA-seq) or tags number for each peaks(ChIP-seq), you will need total reads for TPM or RPKM calculation. Which is the right number of total reads? ChIP-seq: (mapped+unmapped) or just mapped reads which one is the right? And how about RNA-seq? Tha ...
chip-seq rna-seq written 5 weeks ago by mikysyc201610 • updated 5 weeks ago by EagleEye5.6k
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The FDR and P value in RNA-seq analysis
... Hi all, After using edgeR to do RNA-seq analysis, I get p valve and FDR. Which one you will use to select your interest target? I search website more people will recommend FDR value as the cutoff standard. But when read papers, a lot of paper use p value( like -log10P) as y axis to make volcano plot ...
p value and fdr rna-seq written 5 weeks ago by mikysyc201610 • updated 5 weeks ago by doctor.dee005120
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how to normalize tag count to 10 million reads without using homer?
... Hi, I know homer can normalize tag count to 10 million reads but do you know any other methods to do the normalize part except using homer? like macs2 itself, or .... Thanks, ...
chip-seq normalize written 6 weeks ago by mikysyc201610 • updated 6 weeks ago by ATpoint6.5k
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Comment: C: macs2 find different binding sites
... I have rep_1 and rep_2. But I find when i want to find significantly differentially bound sites i need rep_1, rep_2 and rep_3. Do you have good suggestion? Thanks, ...
written 6 weeks ago by mikysyc201610
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Comment: C: A question about "Call differential binding events"
... Hi Kevin, If I use -l = fragment length i used as callpeaks and use -g as 100. i get 11294 peaks in common.bed and get 4692 peaks in con1.bed and get 2174 peaks in con2.bed. But I get 18347 peaks in con1 narrow.peaks and get 31410 peaks in con2 narrow.peaks. SO 11294+4692<18347 and 11294+2174< ...
written 6 weeks ago by mikysyc201610
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Comment: C: macs2 find different binding sites
... I do not have enough replicate, otherwise i will use diffbind. ...
written 6 weeks ago by mikysyc201610
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how i get get same length of peaks by macs2
... Hi, I find after i run macs2, i will get different zise of each peak. if i want to get peaks' length is 200, what kind of command I can use? Thanks ...
macs2 chip-seq written 6 weeks ago by mikysyc201610

Latest awards to mikysyc2016

Rising Star 8 weeks ago, created 50 posts within first three months of joining.
Scholar 9 weeks ago, created an answer that has been accepted. For A: how to use igvtools on ubuntu

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