User: ZZzzzzhong

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ZZzzzzhong150
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4 months, 3 weeks ago
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Posts by ZZzzzzhong

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How to input data for DESeq2 from individual HTSeq count?
... Just like the variable condition sampleFiles <- c('cowan1','cowan2','cowan3','isolate1','isolate2','isolate3') remember sampleFiles correspond with condition ...
written 8 weeks ago by ZZzzzzhong150
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Answer: A: How to input data for DESeq2 from individual HTSeq count?
... directory <- "/path/to/your/files/" directory is where your htseq-count output files are located. sampleFiles <- grep("Bacteria",list.files(directory),value=TRUE) samplesFiles is a variable which points to your htseq-count output files, condition <- c('Bacteria1','Bacteria1',' ...
written 8 weeks ago by ZZzzzzhong150
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Answer: A: 2 peak files in plotAvgProf2 [ChIPseeker]
... files <- list(peak2,peak3) promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000) tagMatrixList <- lapply(files, getTagMatrix, windows=promoter) plotAvgProf(tagMatrixList, xlim=c(-3000, 3000)) ...
written 9 weeks ago by ZZzzzzhong150
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Answer: A: How to get strand information in the bed file of macs1.4 peak calling output?
... Transcriptome usually comes from fixed chains.peak_result is your MACS out put and genes.gtf is your annotation file. intersectBed -wo -a peak_result -b genes.gtf | awk -v OFS="\t" '{print $1,$2,$3,"*","*",$10}'|uniq > Peaks.bed fastaFromBed -s -f genome.fa -bed Peaks.bed -fo Peaks.fa ...
written 9 weeks ago by ZZzzzzhong150
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Answer: A: The m6A-Seq analysis
... It's not very exactly to apply s standard Chip-Seq analysis pipeline to m6A-Seq analysis.RNA' expression is dynamic.So the distribution model is different with chipseq'data(exomePeak is designed to call peaks of m6A seq).m6Aseq belong to RNA which involves the splicing site, it's best to use RNA ali ...
written 9 weeks ago by ZZzzzzhong150
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Comment: C: Is it possible to visualize ChIP peaks of three different samples in one plot us
... if you want to label 1_peak as name1(Any name you want) you can do that`files <- list(name1=1_peak,name2=2_peak,name3=3_peak)` ...
written 9 weeks ago by ZZzzzzhong150
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Answer: A: Is it possible to visualize ChIP peaks of three different samples in one plot us
... This is easy to implement by CHIPseeker. Let's say 1_peak,2_peak and 3_peak are your peak_file. files <- list(1_peak,2_peak,3_peak) peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb,tssRegion=c(-3000, 3000), verbose=FALSE) plotDistToTSS(peakAnnoList) + theme(plot.title = eleme ...
written 9 weeks ago by ZZzzzzhong150
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Answer: A: Data Sorting R
... You can define a new column: df$3 = df$1 * df$2 then df <- subset(df, df$3 < 0, select = 1:2) ...
written 9 weeks ago by ZZzzzzhong150 • updated 9 weeks ago by zx87546.1k
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Answer: A: Can be merged biological replicates?
... > For the experiment with several replicates, it is recommended to > concatenate several ChIP-seq treatment files into a single file. To do > this, under Unix/Mac or Cygwin (for windows OS), type: `$ cat replicate1.bed replicate2.bed replicate3.bed > all_replicates.bed` For BAM or SAM ...
written 11 weeks ago by ZZzzzzhong150 • updated 11 weeks ago by ATpoint11k
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Answer: A: Best method to do clustering (sub-group) single cell RNA-Seq data?
... you can try Seurat(https://satijalab.org/seurat/pbmc3k_tutorial.html).it only need the genecount matrix,then you could do clustering ,DE,and so on ...
written 4 months ago by ZZzzzzhong150

Latest awards to ZZzzzzhong

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Is it possible to visualize ChIP peaks of three different samples in one plot us
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Is it possible to visualize ChIP peaks of three different samples in one plot us

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