<![CDATA[BOL: Wire posts tagged with 'bed']]> https://bioinformaticsonline.com/thewire/tag/bed? https://bioinformaticsonline.com/thewire/view/38653 Thu, 10 Jan 2019 09:25:01 -0600 https://bioinformaticsonline.com/thewire/view/38653 <![CDATA[Wire post by Rahul Nayak]]> Merge overlapping bed file https://bedtools.readthedocs.io/en/latest/content/tools/merge.html #bed #merge #overlapping

]]> Rahul Nayak https://bioinformaticsonline.com/thewire/view/38651 Thu, 10 Jan 2019 09:20:37 -0600 https://bioinformaticsonline.com/thewire/view/38651 <![CDATA[Wire post by Rahul Nayak]]> make a window of 60k of bed file. $ bedtools makewindows -g genome -w 60000 > 60K.windows.bed #bed #bin #window

]]> Rahul Nayak https://bioinformaticsonline.com/thewire/view/37949 Thu, 18 Oct 2018 09:00:03 -0500 https://bioinformaticsonline.com/thewire/view/37949 <![CDATA[Wire post by Neel]]> BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed #Bed #bam #bamToBed #convert

]]> Neel https://bioinformaticsonline.com/thewire/view/35933 Wed, 14 Mar 2018 10:31:04 -0500 https://bioinformaticsonline.com/thewire/view/35933 <![CDATA[Wire post by Rahul Nayak]]> Get the sequences using coordinates in bed file. $ bedtools getfasta -fi input_file.fa -bed regions_file.bed #Bed #Extract #Sequence #bedtools

]]> Rahul Nayak https://bioinformaticsonline.com/thewire/view/31432 Wed, 08 Mar 2017 08:11:52 -0600 https://bioinformaticsonline.com/thewire/view/31432 <![CDATA[Wire post by Jit]]> Get the fasta sequence of the coordinates http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #Bedtools

]]> Jit