User: shrinka.genetics

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Posts by shrinka.genetics

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CHIP Seq Analysis by DiffBind Package
... Hi I am using DiffBind package for CHIP Seq Analysis I have made a sample sheet for input. **My samples have different dimension**. This error is coming. Have anyone ever faced this problem? > library(DiffBind) > Data <- dba(sampleSheet="SampleSheet.txt") 1 NA raw Error in if (is. ...
R chip-seq written 7 days ago by shrinka.genetics0 • updated 4 days ago by Rory Stark880
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CHIP Seq Analysis by DiffBind Package
... Hi I am working on ChipSeq data of histone marks. I am using Diffbind package. I have 8 samples in 2 groups each. I am trying to see differential peak enrichment in these two groups. I have used this to read one file at a time. How can I club 4 samples so that I can do a group comparison? be ...
chip-seq written 6 weeks ago by shrinka.genetics0 • updated 29 days ago by Rory Stark880
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"MethylKit" package for WGBS data
... I am using MethyKit package for WBGS data analysis. There it has a step like > meth <- unite(myobj, destrand=FALSE) uniting... Where it unites, if I put destrand=TRUE, then it gives this error > meth=unite(myobj, destrand=TRUE) destranding... Error in `$<-.data.frame`(`*tmp*`, "stran ...
next-gen sequencing written 8 weeks ago by shrinka.genetics0
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Generation of Dendogram on WGBS data
... Hi I am working on WGBS data and using MethylKit package. Methykit has its own function to make a dendogram on CpG methylation, but I need bootstraping on it. I used these codes. > library(methylKit) > file.list = list (........) > myobj = methRead (file.list, sample.id = list (.... ...
sequencing written 10 weeks ago by shrinka.genetics0 • updated 15 days ago by iwwilson0
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"MethylKit" package for WGBS data
... Hello I am working on WGBS data using MethylKIT package. I am trying to analyse few samples whose dimension are not same (see below). What kind of measure can be taken to handle this type of problem >library(methylKit) > file.list = list ("JChr21-modd.txt","SChr21-modd.txt","Delta2 ...
next-gen sequencing written 3 months ago by shrinka.genetics0
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"MethylKit" package for WGBS data
... Hello I am using MethylKIT package for WGBS Data analysis. There I have observed that whatever input I am giving, in the meth object, actually a certain percent of input data is going for downstream analysis. Chr base strand coverage freqT freqC 53297621 ...
next-gen sequencing written 3 months ago by shrinka.genetics0 • updated 6 weeks ago by Biostar ♦♦ 20
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"MethylKit" package for WGBS data
... Hello I am working with WGBS data and I am using MethylKit package. There in the Descriptive statistics per sample. (a) Histogram of %methylation per cytosine for a sample, I got most of the bases have either high or low methylation. Specially 0% methylation is highest and 100% methylation is lowe ...
next-gen sequencing written 3 months ago by shrinka.genetics0 • updated 3 months ago by RamRS30k
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"MethylKit" package for WGBS data
... Hello I am working with WGBS data and using MethyKit package. I have 12 samples in 3 groups. I used codes like > file.list = list ("JChr21-modd.txt", "BChr21-modd.txt", "SChr21-modd.txt", "NChr21-modd.txt","KChr21-modd.txt","EChr21-modd.txt","CChr21-modd.txt","PChr21-modd.txt", ...
next-gen sequencing written 3 months ago by shrinka.genetics0 • updated 3 months ago by Friederike6.5k
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Annotation Related after WGBS Data Analysis
... I am working with WGBS Data. I got a list of differentially methylated CpGs. I have done the annotation. I have downloaded ref file from UCSC and then merged it with my output file, which had coordinates. Now I got list of differentially methylated CpGs with coordinates and identifier (like NM or N ...
next-gen sequencing written 4 months ago by shrinka.genetics0
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WGBS Annotation Related
... Hello I have a list of differentially methylated CpGs. I just want to upload or paste these coordinates in browser like UCSC etc to get gene name corresponding to these. I just have coordinates of these, not any identifier. Is there any direct method, so that I will get gene names as output when ...
next-gen sequencing written 4 months ago by shrinka.genetics0 • updated 4 months ago by cpad011214k

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