Awk

sort with header maintained

We usually want to maintain header when we do something for the body of the text.\ You can find a body function here which can only accept streams and…

Using Awk to format the gene expression file to gct format for Gene Set Enrichment Analysis (GSEA)

After one runs microarray or RNA-seq analysis, usually he would do a Gene Set Enrichment Analysis (GSEA) analysis. There are many tools to use. One of the…

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…

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:

manipulate GTF file with AWK

AWK is awesome! or I should say linux is awesome!\ I had a post for linux one-liners here useful unix one liners for bioinformatics

useful unix one liners for bioinformatics

I have been using ubuntu 12.04LTS for one year, and I really love it and do not look back at windows at all. Currently, I have dual booting system for linux…

group the same ID to the same line by python, use awk to do SQL like groupby and sum

I was on Seqanswer forum and found someone asked a question:\ \ “Hi guys,\ i hv got a GO file for my differentially expressed genes file, it goes like:

Awk Command to Count Total, Unique, and the Most Abundant Read in a FASTQ file

I was reading through a paper on comparative ChIP-Seq when I found this awk gem that lets you get some very basic stats very quickly on next generation…

awk for simple text manipulation

let’s say you have a bed file (tab delimited):