User: mikysyc2016

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mikysyc201680
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Posts by mikysyc2016

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spike-in Single cell RNA-seq
... Hi all, I need to define control features (genes) - ERCC spike-ins and mitochondrial genes when I do single cell RNA-seq analysis. while isSpike in SingleCellExperiment package defunct now. isSpike(umi, "ERCC") <- grepl("^ERCC-", rownames(umi)) isSpike(umi, "MT") <- rownames(umi) %in% ...
R rna-seq sequencing written 8 months ago by mikysyc201680
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Comment: C: how to get distance of each SNPs to the transcripts' 5'UTR and 3'UTR?
... when I use UCSC to upload my transcripts list, then I get a table which include transcript start point and end point, while when i use txend-txstart which is much much longer than the length of that mRNA. Do you know the reason? Thanks. ...
written 8 months ago by mikysyc201680
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how to get distance of each SNPs to the transcripts' 5'UTR and 3'UTR?
... Hi all, I have a SNPs list which are inside of different transcripts respectively(I have their related transcript list). And I also know the accurate chromosome location of the every SNP. Now I want to know the distance of that SNP to its transcripts' 5'UTR's beginning and 3'UTR's ending . how ...
genome R sequence snp sequencing written 8 months ago by mikysyc201680 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: mm9 RNA-seq reference genome
... I see. Thanks a lot! ...
written 2.3 years ago by mikysyc201680
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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 2.3 years ago by mikysyc201680
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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 2.3 years ago by mikysyc201680
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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 2.3 years ago by mikysyc201680
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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 2.4 years ago by mikysyc201680 • updated 2.4 years ago by Kevin Blighe69k
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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 2.5 years ago by mikysyc201680 • updated 2.5 years ago by reskejak30
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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 2.5 years ago by mikysyc201680

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Popular Question 7 months ago, created a question with more than 1,000 views. For How to know the mm9 genome size?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to know the mm9 genome size?
Popular Question 8 months ago, created a question with more than 1,000 views. For download mm9 mouse genome fasta file
Great Question 19 months ago, created a question with more than 5,000 views. For How to use igv on ubuntu
Great Question 19 months ago, created a question with more than 5,000 views. For samtools sort bam file
Popular Question 19 months ago, created a question with more than 1,000 views. For How to use igv on ubuntu
Popular Question 19 months ago, created a question with more than 1,000 views. For download mm9 mouse genome fasta file
Popular Question 19 months ago, created a question with more than 1,000 views. For How to use MACS2 to do peak calling
Popular Question 19 months ago, created a question with more than 1,000 views. For Homer motif analysis
Popular Question 2.3 years ago, created a question with more than 1,000 views. For The FDR and P value in RNA-seq analysis
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to use igv on ubuntu
Popular Question 2.3 years ago, created a question with more than 1,000 views. For samtools sort bam file
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