User: mikysyc2016

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mikysyc201630
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3 months, 3 weeks ago
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7 months, 4 weeks ago
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Posts by mikysyc2016

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Comment: C: mm9 RNA-seq reference genome
... I see. Thanks a lot! ...
written 4 months ago by mikysyc201630
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Comment: C: mm9 RNA-seq reference genome
... Thank you! That make sense.I prepare to use kallisto to align the reads which I can run my personal computer. Can I use the link you provide(Are they reference genome or reference cDNA transcriptome)? ...
written 4 months ago by mikysyc201630
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Comment: C: mm9 RNA-seq reference genome
... Thank you. Can I use them for standard RNA-seq analysis? What is the difference between genome FASTA( I think genome FASTA is for DNA-seq) and reference cDNA FASTA? WHich one I can use? And what is the difference if I download GTF or FASTA? Thanks in advance. ...
written 4 months ago by mikysyc201630
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Comment: C: mm9 RNA-seq reference genome
... I want to do standard RNA-seq analysis. FTP has DNA fasta and cDNA fasta, but they do not show mm9 or mm10. Depend on that I think I need cDNA reference for RNA-seq analysis. And I think genome reference is for DNA-seq analysis( like ChIP-seq...). Did I misunderstand? Thanks! ...
written 4 months ago by mikysyc201630
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mm9 RNA-seq reference genome
... Hi all If I want to align my RNA-seq reads to mm9 cDNA reference. How I download this fasta file? Thanks in advance, Yachen ...
gene tutorial alignment rna-seq sequencing written 4 months ago by mikysyc201630 • updated 4 months ago by Kevin Blighe35k
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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 5 months ago by mikysyc201630 • updated 5 months 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 6 months ago by mikysyc201630
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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 6 months ago by mikysyc201630
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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 6 months ago by mikysyc201630 • updated 6 months ago by EagleEye6.1k
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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 6 months ago by mikysyc201630 • updated 6 months ago by Dattatray Mongad240

Latest awards to mikysyc2016

Rising Star 7 months ago, created 50 posts within first three months of joining.
Scholar 7 months ago, created an answer that has been accepted. For A: how to use igvtools on ubuntu

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