FASTQ

Sometimes, you get a processed bam file from other resources, but you want to map it with another aligner. For example, the old BWA aln does not keep the…

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…

I passed my defense on Tuesday, and now I am a PhD! what a long process, it took me six years. I’ve been enjoying the PhD experience though.

I was looking at some old ChIP-seq data with raw file in qseq format. I want to convert them to fastq file for mapping with bowtie.

#print out the first two lines of every 4 lines. -n flag suppress all of the other lines and only print the line\ you specified. -e option tells sed to…

it is developed by Heng Li in princeton.

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…

While browsing SeqAnswers.com today I came across a post where Uwe Appelt provided a couple of lines of Unix shell wizadry to solve some problem. What…