User: pradyumna Jayaram

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Manipal, School Of Life Sciences
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https://techstatus.in/
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@pradyumnasagar
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Posts by pradyumna Jayaram

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How to run EXCAVATOR2?
... Even I didn't run any R script myself, those scripts are run by perl wrapper, there are some R scripts in the folder. If you are getting the exact same error then change the value. or else update your R version and check back. It would be helpful if you provide the error message you are getting. ...
written 7 months ago by pradyumna Jayaram200
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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 9 months ago by pradyumna Jayaram200
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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 9 months ago by pradyumna Jayaram200
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Comment: C: Differential gene expression Analysis - sample Size
... great! Thank you very much. ...
written 12 months ago by pradyumna Jayaram200
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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 12 months ago by pradyumna Jayaram200
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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 12 months ago by pradyumna Jayaram200
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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 12 months ago by pradyumna Jayaram200
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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 12 months ago by pradyumna Jayaram200
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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 23 months ago by pradyumna Jayaram200
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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 23 months ago by pradyumna Jayaram200 • updated 23 months ago by erwan.scaon720

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Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How to run EXCAVATOR2?

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