How to take sample peak from each chromosome in peak bed files ?
1
0
Entering edit mode
@jurat-shahidin-9488
Last seen 4.1 years ago
Chicago, IL, USA

Hi,

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 :

myPkg
- 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 :

Jurat

r chipseq encode peak • 1.5k views
ADD COMMENT
0
Entering edit mode
@federicocomoglio-4524
Last seen 6.9 years ago
Switzerland

Hi Jurat,

this discussion might be of help: https://www.biostars.org/p/85063/

Federico

ADD COMMENT
0
Entering edit mode

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 :

Jurat

ADD REPLY

Login before adding your answer.

Traffic: 545 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6