https://divingintogeneticsandgenomics.com/tags/genomic-interval/ Recent content in Genomic Interval on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Tue, 24 Sep 2013 10:52:00 -0700 https://divingintogeneticsandgenomics.com/archive/finding-the-closest-feature-given-a-set-of-genomic-coordinates/ Tue, 24 Sep 2013 10:52:00 -0700 https://divingintogeneticsandgenomics.com/archive/finding-the-closest-feature-given-a-set-of-genomic-coordinates/ I have a bed file which contains peak information for a ChIP-seq data. I want to find the genes that are closest to these peaks. I am aware that many softwares can do this job. cistrome-Galaxy pipeline http://cistrome.org/ap/ from shirley liu's lab in Harvard, bioconductor package ChIPpeakAnno http://www.bioconductor.org/packages/2.12/bioc/html/ChIPpeakAnno.html are tools can deal with this kind of task. In addition to them, bedtool is a very good tool for Genomic Interval manipulation. https://divingintogeneticsandgenomics.com/archive/genomic-interval-tree-interval-manipulation/ Fri, 20 Sep 2013 14:14:00 -0700 https://divingintogeneticsandgenomics.com/archive/genomic-interval-tree-interval-manipulation/ we do a lot of work on overlapping genomic features. Bedtool is a great tool for this kind of task, but sometimes I want to implement it with python for some custom usage. I found many useful links below. I have to digest them to fully understand how the tree is constructed. http://informatics.malariagen.net/2011/07/07/using-interval-trees-to-query-genome-annotations-by-position/ http://blog.nextgenetics.net/?e=45 http://hackmap.blogspot.com/2008/11/python-interval-tree.html http://psaffrey.wordpress.com/2011/04/ http://www.biostars.org/p/2244/ I am by no means familiar with those algorithms. Have a peek how other people do it, and learn from them is a good start for me. https://divingintogeneticsandgenomics.com/archive/find-exons-introns-and-intergenic-regions/ Fri, 17 May 2013 11:13:00 -0700 https://divingintogeneticsandgenomics.com/archive/find-exons-introns-and-intergenic-regions/ see post here: http://davetang.org/muse/2013/01/18/exons-introns-and-intergenic-regions/ Exons, introns and intergenic regions Posted on January 18, 2013 by Davo I'm interested in defining the exons, introns and intergenic regions of the genome based on GENCODE. So I thought about a fuss free way to do this, and BEDTools would be perfect. Download the latest GENCODE annotations (version 14): 1 wgetftp://ftp.sanger.ac.uk/pub/gencode/release_14/gencode.v14.annotation.gtf.gz I will use mergeBed, subtractBed and complementBed. https://divingintogeneticsandgenomics.com/archive/genomic-interval-manipulation/ Tue, 02 Apr 2013 20:02:00 -0700 https://divingintogeneticsandgenomics.com/archive/genomic-interval-manipulation/ # for manipulation of Genomic Intervals # you can use Galaxy https://main.g2.bx.psu.edu/, #Bedtools http://bedtools.readthedocs.org/en/latest/content/overview.html #or Bioconductor package GenomicRanges #http://stuff.mit.edu/afs/athena/software/r_v2.14.1/lib/R/library/GenomicRanges/html/00Index.html #python package HTSeq http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#tour http://psaffrey.wordpress.com/2011/04/ Peter Saffrey's Weblog Scientific computing and bioinformatics. Overlapping Genomic Intervals Revisited April 5, 2011 I’ve posted before on finding the right approach to overlapping genomic intervals. Broadly speaking, the problem is this: you have two sets of intervals, where each interval is (chromosome, start, end). You want to know where the intervals in the first set overlap the intervals in the second set.