https://divingintogeneticsandgenomics.com/tags/sed/ Recent content in Sed on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Tue, 23 Jun 2015 12:30:00 -0700 https://divingintogeneticsandgenomics.com/archive/chip-seq-analysis-part1/ Tue, 23 Jun 2015 12:30:00 -0700 https://divingintogeneticsandgenomics.com/archive/chip-seq-analysis-part1/ sofware installation and data source install MACS2: 06/11/2015 sudo pip -H install MACS2 macs2 version:2.1.0.20150420 install NCIS to estimate the scaling factor: Download the package here: wget http://www.biomedcentral.com/content/supplementary/1471-2105-13-199-s2.gz It is a .gz file, you can open your Rstudio and install it: install.packages("~/NCIS/1471-2105-13-199-s2.gz", repos = NULL, type="source") For help: library(NCIS); ?NCIS see a post here using NCIS before MACS peak calling: Adding a custom normalization to MACS. when use NCIS, one needs to deduplicate the reads first. https://divingintogeneticsandgenomics.com/archive/everyone-will-write-a-blog-post-on-dplyr/ Fri, 26 Sep 2014 12:28:00 -0700 https://divingintogeneticsandgenomics.com/archive/everyone-will-write-a-blog-post-on-dplyr/ dply is a nice R package to manipulate big data. There are several good tutorials I came across: http://www.dataschool.io/dplyr-tutorial-for-faster-data-manipulation-in-r/ http://stat545-ubc.github.io/block009_dplyr-intro.html http://stat545-ubc.github.io/bit001_dplyr-cheatsheet.html http://gettinggeneticsdone.blogspot.com/2014/08/do-your-data-janitor-work-like-boss.html I followed the example in the early edition of Bioinformatics Data Skills on the dplyr part and put a gist below. The example used dplyr to manipulate and summarize the human annotation gff file downloaded here http://useast.ensembl.org/info/data/ftp/index.html. I downloaded the ensemble 74 build which is different from the 75 build in the example of the book. https://divingintogeneticsandgenomics.com/archive/rename-a-bunch-of-files-with-bash-by-regular-expression/ Thu, 14 Aug 2014 07:44:00 -0700 https://divingintogeneticsandgenomics.com/archive/rename-a-bunch-of-files-with-bash-by-regular-expression/ I am at the MSU NGS 2014 course. My colleague wanted to follow the khmer protocol with his own data, but one of the steps has to use a certain file name convention. In the protocol it requires fastq files listed as: *001_R1.fastq.gz 001 is the replicate number, it can be 002 or 003 or any number of replicates you have. ( for RNA-seq, sequence as many as biological samples as possible !