Bed on Chatomics https://divingintogeneticsandgenomics.com/tags/bed/ Recent content in Bed on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Wed, 16 May 2018 13:16:00 -0700 get the peaks that shared in multiple samples https://divingintogeneticsandgenomics.com/archive/get-the-peaks-that-shared-in-multiple-samples/ Wed, 16 May 2018 13:16:00 -0700 https://divingintogeneticsandgenomics.com/archive/get-the-peaks-that-shared-in-multiple-samples/ View this gist on GitHub read in all the files in a folder to R https://divingintogeneticsandgenomics.com/archive/read-in-all-the-files-in-a-folder-to-r/ Sun, 07 Feb 2016 20:14:00 -0800 https://divingintogeneticsandgenomics.com/archive/read-in-all-the-files-in-a-folder-to-r/ Ming Tang February 7, 2016 read in all the files in a folder with a loop see a post I downloaded some broadpeak data from UCSC and put them in a folder /Users/mtang1/projects/ENCODE_ChIPseq/data/ I cut only first four columns of those files and How can I read in all the bed files as GRanges? # the base of the path cancer.base<- "/Users/mtang1/projects/ENCODE_ChIPseq/data" # list.files will print out all the files in the folder ending with broadPeak cancer. Using Awk to join two files based on several columns https://divingintogeneticsandgenomics.com/archive/using-awk-to-join-two-files-based-on-several-columns/ Thu, 14 May 2015 14:35:00 -0700 https://divingintogeneticsandgenomics.com/archive/using-awk-to-join-two-files-based-on-several-columns/ I was reading a thread on stackoverflow and found that this post was very interesting. I will go through the problem and the awk solution. Again, Awk is awesome! Note: It looks a bit messy when I copied the ipython notebook directly into Blogger. Ideally, one can write the blog using ipython notebook directly, but it does not work well with Blogger. see here http://blog.fperez.org/2012/09/blogging-with-ipython-notebook.html I do not want to use other blogging platforms for now. how to get a genome-wide motif bed file https://divingintogeneticsandgenomics.com/archive/how-to-get-a-genome-wide-motif-bed-file/ Thu, 13 Feb 2014 07:13:00 -0800 https://divingintogeneticsandgenomics.com/archive/how-to-get-a-genome-wide-motif-bed-file/ Someone was asking this question on Seqanswers http://seqanswers.com/forums/showthread.php?t=40762&highlight=genome+motif+bed For motif analysis, the most popular program is MEME http://meme.nbcr.net/meme/ There are a bunch of tools in the suites including some useful ones for ChIP-seq I also saw RAST http://rsat01.biologie.ens.fr/rsa-tools/index.html and oPOSSUM were mentioned http://opossum.cisreg.ca/oPOSSUM3/ I analyze ChIP-seq data a lot. Usually, one gets a bed file containing the positions of the peaks. However, many motif analysis programs require fasta file as input.