User: vkgaur25

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vkgaur2530
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Posts by vkgaur25

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Using data.matrix while reading raw counts from a csv file for DESeq2 analysis
... Problem solved. Thanks a lot ...
written 5 days ago by vkgaur2530
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Using data.matrix while reading raw counts from a csv file for DESeq2 analysis
... Hi all, I have my raw read counts in a csv file and while doing DESEq2 I read it like- calidata<-read.csv("/Users/XXX/Desktop/xxx/TT48.csv", header=TRUE, row.names = 1) mat_data <- data.matrix(calidata) and then proceeded with DESeq2. If I use same input file but in a tab deli ...
rna-seq written 5 days ago by vkgaur2530 • updated 5 days ago by Kevin Blighe24k
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Plot norm counts for all genes in two conditions
... Hi, I have norm counts from DESeq2 and I want to see the abundance of all genes (miRNAs in my case) in males and females. I think I should look at the normalized counts (or raw counts?) separately in males and females. I want to plot norm counts of all genes in two condition (m/f). IHow can I do it ...
rna-seq written 7 days ago by vkgaur2530 • updated 5 days ago by Kevin Blighe24k
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miRNA structure file (hairpin structure) from precursor miRNA sequences
... Hi, Probably this is a bit outside of the kinds of questions asked here but I am unable to find any suitable answer of my question so asking here. I have RNA-Seq data and I am looking for isomiRs . For alignment step I need a hairpin fasta file and a structure file (Mirna.str) . I know both of these ...
rna-seq written 16 days ago by vkgaur2530 • updated 16 days ago by toralmanvar420
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Box plot for single gene expression for various samples in a given condition ( male/female)
... Hi All Can some help me with box plot? I used DESeq2 for DE analysis and now I want to plot box plots for some most highly DE genes. Since I am trying to see the difference of expression in sex (male/female) , I want box plot where there are two box plots for same gene in two condition (male/female ...
rna-seq written 24 days ago by vkgaur2530 • updated 24 days ago by Devon Ryan81k
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How to calculate read frequency from raw count data
... Hi all I am dealing with RNA Seq data and I have raw read counts of 13 samples. I want to have a read frequency table as I want to see the most abundant miRNAs among list of thousands of miRNAs produced after mapping step . Is there any way to do it in R/ Bioconductor? Also I need a little clarifica ...
R rna-seq written 28 days ago by vkgaur2530 • updated 28 days ago by Devon Ryan81k
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Comment: C: Error while executing "estimateSizeFactors" from DESeq2
... Thank you so much Kevin. It worked well. :) ...
written 4 weeks ago by vkgaur2530
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Error while executing "estimateSizeFactors" from DESeq2
... Hi all, I am using DESeq2 for DE analysis and I want to normalize my read counts on the basis of two calibrator set (their counts) that were used. I am using estimateSizeFactors to give the read counts of calibrators as "controlGenes" so that I can run DESeq2 but when I execute my codes (which are ...
software error R deseq2 written 4 weeks ago by vkgaur2530 • updated 4 weeks ago by zx87544.7k
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miraligner gives zero annotated reads.
... Hi I am new to isomiR analysis and I tried using miraligner with fastq sequences produced from small RNA seq. I have couple of issues- 1. When I run my script- java -jar miraligner.jar -sub 1 -trim 3 -add 3 -s hsa -i /Users/pg2597/Downloads/pilot_fastq/xyz.fastq -db DB -o /Users/pg2597/Desktop/outp ...
rna-seq written 7 weeks ago by vkgaur2530
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Idea about increasing coverage in sequencing
... I likely need a 100x increase in the number of reads per Amplicon (using amplicon library) . Can you guys provide ideas of doing that? One option could be to create a new amplicon library with 1/10 the number of amplicons but still need to get the additional 10x improvement. Any idea? ...
sequencing written 10 weeks ago by vkgaur2530

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