Question: How to take sample peak from each chromosome in peak bed files ?
gravatar for Jurat Shahidin
3.0 years ago by
Chicago, IL, USA
Jurat Shahidin70 wrote:


I used data set from Encode consortium for my package development, due to size of actual peak files are rather big, I can't use these data set for my package use. Because actual size of Bioconductor package resulted from R CMD build must be less than 4Mb on disk, I have to use rather small peak file as an example data for my package . In Encode sample's data set, each peak files contains around 100,000 peaks each. How can I obtain small example data of Chip-seq peak files ? Is there any approach getting ideal example data from actual peak files for package use? Thanks in advance :)

Here is quick insight of my actual peak files in my packages :

- inst
     - extdata
             - wgEncodeOpenChromChipK562CmycAlnRep1.bed
             - wgEncodeOpenChromChipK562CmycAlnRep2.bed
             - wgEncodeOpenChromChipK562CmycAlnRep3.bed
             - wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep1.bed
             - wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep2.bed
             - wgEncodeSydhTfbsK562CmycIfna30StdAlnRep1.bed
             - wgEncodeSydhTfbsK562CmycIfna30StdAlnRep2.bed
             - wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep1.bed
             - wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep2.bed
             - wgEncodeSydhTfbsK562CmycIggrabAlnRep1.bed
             - wgEncodeSydhTfbsK562CmycIggrabAlnRep2.bed
             - wgEncodeSydhTfbsK562CmycStdAlnRep1.bed
             - wgEncodeSydhTfbsK562CmycStdAlnRep2.bed
- R


Edit :

I am looking at Chip-seq for transcription factors.  how can I get small peak files such as each bed file has around 1000 peaks ? 

Should I take sample from each chromosome in each peak file ? How to get sample ? Any approach to get ideal, small example data from Chip-seq peak files? Thanks a lot

Best regards :


chipseq R encode peak • 630 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Jurat Shahidin70
Answer: How can I get rather small example data from Encode sample's Chip-seq peak file
gravatar for federico.comoglio
3.0 years ago by
federico.comoglio100 wrote:

Hi Jurat,

this discussion might be of help:


ADD COMMENTlink written 3.0 years ago by federico.comoglio100

Hi Federico :

Thanks for this post from Biostar. Not familiar with using BEDOPS tools on windows. How can I facilitate the process of taking samples from each bed files ? I think  it will take some time to get familiar with BEDOPS tools and try the solution. I need something fast, general approach instead. Any idea ?

Best regards :


ADD REPLYlink written 3.0 years ago by Jurat Shahidin70
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