User: prakash

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prakash100
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Posts by prakash

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Doing GSEA analysis on a set of genes
... you can follow the steps provided in this [link][1] [1]: https://www.biostars.org/p/279097/#279127 ...
written 6 weeks ago by prakash100
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Comment: C: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca
... > grep -v "#" peak.txt |cut -f 2-4,1,6 > peak1.bed Actually, using this code, order of column will not be changed. So, yes below shorter code which you mentioned will solve the purpose. cut -f 1-6 peaks.txt | awk '{print $2,$3,$4,$1,$5}' OFS="\t" ...
written 7 weeks ago by prakash100
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Comment: C: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca
... > but still 1 questions: "#" mean any pattern I can input, is that > right? I didnot use it yes, within double quote, you can use any pattern. in this case, line with comment in peak file i.e "#" is not required, so to filter it, "grep -v "#" has been used. ...
written 7 weeks ago by prakash100
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Answer: A: Gene Set Enrichment Analysis after DESeq2
... Hi Sreeraj Genes can be ranked based on fold change and P value and that can be used in GSEA package. you can use this R code for this purpose. x <- read.table("DE_genes.txt",sep = "\t",header = T) head(x) x$fcsign <- sign(x$log2.fold_change.) x$logP=-log10(x$p_value) ...
written 7 weeks ago by prakash100
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Answer: A: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca
... simple "grep" and "awk" can do your job. grep -v "#" peak.txt |cut -f 1,2,3,4,6 | awk '{print $2"\t"$3"\t"$4"\t"$1"\t"$5}' >peak.bed ...
written 7 weeks ago by prakash100
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Comment: C: Motif database of choice
... Jaspar and TRANSFAC are used widely I guess.. ...
written 3 months ago by prakash100
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Comment: A: Nomalize chip-seq data
... Is your 3 ChIPseq dataset for different factor/histone or same factor/histone in different condition ? ...
written 3 months ago by prakash100
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Answer: A: Explanation of BETA output
... Have you put this question in [BETA google group][1] ? [1]: https://groups.google.com/forum/#!forum/cistromebeta ...
written 3 months ago by prakash100
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Answer: A: How to find out whether Chip-seq peaks falls within promoter or enhancer region
... use [homer][1], you can define the peaks based on "distance to TSS" column as promoter or enhancer. [1]: http://homer.ucsd.edu/homer/ngs/annotation.html ...
written 3 months ago by prakash100
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Answer: A: Cuffnorm: which output file should I use
... genes.fpkm_tracking is the file for genes with its normalized FPKM (fragment per kb per millions of mapped reads) ...
written 3 months ago by prakash100

Latest awards to prakash

Scholar 7 weeks ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 9 weeks ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value
Popular Question 3 months ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value

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