User: lhaiyan3

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lhaiyan320
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United States
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3 months ago
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2 years, 8 months ago
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l*******@gmail.com

Posts by lhaiyan3

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Tool to annotate ChIP-Seq peaks (hg19 or mm10) and find neighboring peaks from m
... Hi, Abhishek: I tried to use the peak-tool and got the output correctly. But I noticed all the INTERGENICE and ENHANCER, ENHANCER-SUPER did not have the correlate gene, distance to TSS, but the PROMOTER annotation has all this information, did you have way to add these information? Thanks. HY chr ...
written 3 months ago by lhaiyan320
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ngsplot-how to get multiplot around the IP peak region and the genes nearest to peak region?
... Dear all, I have the 3 IP (TF1, TF2, TF3) data, and I use mac2 callpeak to get the peak files (TF1.peak). I want to get the multiplot fig about three IP signals at 1, TF1 peak region 2, these IP singals at genes nearest to TF1 peaks . I am not sure what genelist file I should put in the config f ...
chip-seq written 4 months ago by lhaiyan320
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How to do the peakcalling for fly spike-in ChIPseq data
... Dear all, We have the fly spike-in ChIP-seq data, I use the following tab to calculate the correlation factor, File/Sample name DMSO_input Induced_Input DMSO_TF1 Induced_TF1 ChIP target TF1 TF1 Treatment DMSO induced DMSO induced Tags mapped to entire dm3 genome 82,362 84,401 2, ...
chip-seq written 4 months ago by lhaiyan320 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks so much for your quick reply. I got the heatmap fig according to your script. I will following your suggestions to set up the different sub-group. You really help me a lot! best HY ...
written 6 months ago by lhaiyan320
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Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks so much for your script. I followed your biomaRt script and now I can get the gsva enrichment score. Sorry I still have another question about how to get the heatmap. Your protocol is about the disease vs control sample comparison. We just have 16 samples in the dataset, no compar ...
written 6 months ago by lhaiyan320 • updated 6 months ago by Kevin Blighe24k
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Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks very much for your quick reply. I followed your suggestions and got the following wrong message again, can you please help me check? > gsva.scores <- gsva(data.matrix(RPKM), gene.sets, method="gsva", mx.diff=TRUE, verbose=TRUE, rnaseq=TRUE, parallel.sz=8) Error in .local(ex ...
written 6 months ago by lhaiyan320
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How to use GSVA for the RNA-seq RPKM file
... Dear all, I am trying to use GSVA for the RNA-seq analysis. I have the refseq annotation based RPKM files for the RNA-seq. RPKM <- read.table("test.txt",header=TRUE,row.names=1,sep="\t") #C2 collection of curated gene sets that form part of the Molecular Signatures Database (MSigDB) ver ...
rna-seq written 6 months ago by lhaiyan320 • updated 6 months ago by Kevin Blighe24k
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Comment: C: GSVA on RNAseq data
... Hi, colonppg: Can you use GSVA for your RNA-seq RPKM data now? Can you please share your R script with me? I still have a lot problem with it. Thanks very much. HY ...
written 6 months ago by lhaiyan320
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how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
... Dear all: Did anyone use ESTIMATE (http://bioinformatics.mdanderson.org/main/ESTIMATE:Overview) to infer tumor purity and stromal score from RNA-seq before? I am not clear how to use this tool and what is the input file format for this tool? They are just several steps, and i did not figure out ho ...
rna-seq written 8 months ago by lhaiyan320 • updated 4 months ago by sina.nassiri20
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how to extract the RD, AD, VAF information for the normal and tumor samples from the MuTect2 output vcf file?
... Dear all: I have the tumor-normal pair Mutect2 output VCF file. I want to get the DP, RD, AD and VAF information for both tumor and normal samples. Can anyone please give me some suggestions? Thanks very much. best HY ...
exom-seq mutect2 written 11 months ago by lhaiyan320 • updated 11 months ago by Biostar ♦♦ 20

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