User: pradyumna Jayaram

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Manipal, School Of Life Sciences
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Posts by pradyumna Jayaram

<prev • 20 results • page 1 of 2 • next >
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Comment: C: How to call variants for mitochondrial genome data of nanopore minIon sequencing
... No we didnot try any pileup based method, Please suggest what tools can be used for that(samtools mpileup?). We got ~400x coverage for the samples. ...
written 21 days ago by pradyumna Jayaram150
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How to call variants for mitochondrial genome data of nanopore minIon sequencing?
... We tried to call variant using nanopolish but we need to specify the ploidy information, which is where we are stuck. can we give ploidy information as 1? When we give ploidy as 1 we got a warning saying Number of variants in span (62) would exceed max-haplotypes. Variants may be missed. Consi ...
genome mitochondria nanopolish snp nanopore written 22 days ago by pradyumna Jayaram150
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Comment: C: Differential gene expression Analysis - sample Size
... great! Thank you very much. ...
written 3 months ago by pradyumna Jayaram150
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Comment: C: Differential gene expression Analysis - sample Size
... Can we compare 3 normal with 300 tumor sample? CESC in TCGA has only 3 normal samples. ...
written 3 months ago by pradyumna Jayaram150
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Comment: C: How to take input TCGA miRNA data in Limma R package for differential expression
... It seems like the data is for single sample. the same read count is available for multiple samples and can be merged. I'm Guessing to go with DESeq2 or EdgeR for differential analysis. can limma be used for same? which one would be more effitient in identifying differential expression? ...
written 4 months ago by pradyumna Jayaram150
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Comment: C: How to take input TCGA miRNA data in Limma R package for differential expression
... @kevin Yes it is miRNA-seq data from TCGA ...
written 4 months ago by pradyumna Jayaram150
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Comment: C: How to take input TCGA miRNA data in Limma R package for differential expression
... Hi, @skjobs1234 did you find an appropriate answer for your query? Even I'm performing the similar analysis. ...
written 4 months ago by pradyumna Jayaram150
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Comment: C: Tools for Copy Number Variation analysis from ion Proton data.
... I have 10 samples and 1 pooled Control sample will it work good? ...
written 14 months ago by pradyumna Jayaram150
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Tools for Copy Number Variation analysis from ion Proton data.
... Hello Everyone, Can anyone suggest the tool to detection of copy number variation from the data obtained from Ampliseq exome sequencing Iontorrent proton platform. I have tried different tools like Excavator2, cnvkit, FreeC, Ionreporter. Each tool gives different region of CNV from the data. ...
iontorrent-proton ampliseq ngs next-gen cnv written 14 months ago by pradyumna Jayaram150 • updated 14 months ago by erwan.scaon590
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Comment: C: Looking for wig base coverage file for hg19
... Excavator2_v1.1.2 provides ucsc.hg19.bw file, I think you can use ucsc's bigWigToWig utility to convert. I am not sure whether it is a good choice. ...
written 14 months ago by pradyumna Jayaram150

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