how to read.bismark result bam.file

[yizha...@gmail.com]

I analysed my  WGBS data，first I used the Bismark to map the sequence reads to the reference genome, it generated a result file of .bam file. Then , I used Bismark_extaract to call CpG site ,but some file fail to calling .

now I using ,methylKit to read.bismark (processBismarkAln ) , it seem must be sort the bam to sam by chromosme. It displays ,processBismarkAln can read the bam file.But I fail to use the function.

this is my command about processBismarkAln(location=("LZH371L_1.clean_bismark_bt2_pe_sort.bam"),sample.id="LZH371L",assembly="napar",save.folder=getwd(),save.context=c("CpG","CHG","CHH"),read.context=c("CpG","CHG","CHH"))

Is there any error in my command?

another question : I have got the result file about the "CpG.txt ", how to use the result to do the follow analysed , such as the methylation Stats ,and so on.

> getCoverageStats(HLiver_CpG.txt[[1]],plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in getCoverageStats(HLiver_CpG.txt[[1]], plot = TRUE, both.strands = FALSE,  :

  object 'HLiver_CpG.txt' not found

> getCoverageStats(methylRawList.obj[HLiver_CpG.txt],plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in getCoverageStats(methylRawList.obj[HLiver_CpG.txt], plot = TRUE,  :

  object 'methylRawList.obj' not found

> getCoverageStats(object="HLiver_CpG.txt",plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in (function (classes, fdef, mtable)  :

  unable to find an inherited method for function ‘getCoverageStats’ for signature ‘"character

[Altuna Akalin]

Please look at the examples and the vignette, you are trying to run your functions on the text files

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[张毅]

oo，another question, I have got the result about the "bismark_methylation_extractor" CpG. context  and non_CpG.context, if i want to use methylkit to analyse , should i write script to convert the result to methylKit need form? Or there is a function to read the result? I don't understand the function about the "methRead " bisamrk、and bismark...,is that function to analyse the result?

2017-03-22 21:46 GMT+08:00 Altuna Akalin <aak...@gmail.com>:

Please look at the examples and the vignette, you are trying to run your functions on the text files

On Wed, Mar 22, 2017 at 4:33 AM, <yizha...@gmail.com> wrote:

I analysed my  WGBS data，first I used the Bismark to map the sequence reads to the reference genome, it generated a result file of .bam file. Then , I used Bismark_extaract to call CpG site ,but some file fail to calling .

now I using ,methylKit to read.bismark (processBismarkAln ) , it seem must be sort the bam to sam by chromosme. It displays ,processBismarkAln can read the bam file.But I fail to use the function.

this is my command about processBismarkAln(location=("LZH371L_1.clean_bismark_bt2_pe_sort.bam"),sample.id="LZH371L",assembly="napar",save.folder=getwd(),save.context=c("CpG","CHG","CHH"),read.context=c("CpG","CHG","CHH"))

Is there any error in my command?

another question : I have got the result file about the "CpG.txt ", how to use the result to do the follow analysed , such as the methylation Stats ,and so on.

> getCoverageStats(HLiver_CpG.txt[[1]],plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in getCoverageStats(HLiver_CpG.txt[[1]], plot = TRUE, both.strands = FALSE,  :

  object 'HLiver_CpG.txt' not found

> getCoverageStats(methylRawList.obj[HLiver_CpG.txt],plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in getCoverageStats(methylRawList.obj[HLiver_CpG.txt], plot = TRUE,  :

  object 'methylRawList.obj' not found

> getCoverageStats(object="HLiver_CpG.txt",plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in (function (classes, fdef, mtable)  :

  unable to find an inherited method for function ‘getCoverageStats’ for signature ‘"character

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[Altuna Akalin]

You have to read the docs of Bismark it can provide tabular output similar to bedgraph.

Those can be read in by methylKit

On Fri, 24 Mar 2017 at 08:27, 张毅 <yizha...@gmail.com> wrote:

oo，another question, I have got the result about the "bismark_methylation_extractor" CpG. context  and non_CpG.context, if i want to use methylkit to analyse , should i write script to convert the result to methylKit need form? Or there is a function to read the result? I don't understand the function about the "methRead " bisamrk、and bismark...,is that function to analyse the result?

2017-03-22 21:46 GMT+08:00 Altuna Akalin <aak...@gmail.com>:

Please look at the examples and the vignette, you are trying to run your functions on the text files

On Wed, Mar 22, 2017 at 4:33 AM, <yizha...@gmail.com> wrote:

I analysed my  WGBS data，first I used the Bismark to map the sequence reads to the reference genome, it generated a result file of .bam file. Then , I used Bismark_extaract to call CpG site ,but some file fail to calling .

now I using ,methylKit to read.bismark (processBismarkAln ) , it seem must be sort the bam to sam by chromosme. It displays ,processBismarkAln can read the bam file.But I fail to use the function.

this is my command about processBismarkAln(location=("LZH371L_1.clean_bismark_bt2_pe_sort.bam"),sample.id="LZH371L",assembly="napar",save.folder=getwd(),save.context=c("CpG","CHG","CHH"),read.context=c("CpG","CHG","CHH"))

Is there any error in my command?

another question : I have got the result file about the "CpG.txt ", how to use the result to do the follow analysed , such as the methylation Stats ,and so on.

> getCoverageStats(HLiver_CpG.txt[[1]],plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in getCoverageStats(HLiver_CpG.txt[[1]], plot = TRUE, both.strands = FALSE,  :

  object 'HLiver_CpG.txt' not found

> getCoverageStats(methylRawList.obj[HLiver_CpG.txt],plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in getCoverageStats(methylRawList.obj[HLiver_CpG.txt], plot = TRUE,  :

  object 'methylRawList.obj' not found

> getCoverageStats(object="HLiver_CpG.txt",plot=TRUE,both.strands=FALSE,labels=TRUE)

Error in (function (classes, fdef, mtable)  :

  unable to find an inherited method for function ‘getCoverageStats’ for signature ‘"character

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