I started to learn bioinformatics because I needed to analyze public ChIP-seq data in 2012. That’s how I got to know Shirley Liu’s lab at Dana-Farber Cancer Institute.
And God knows that I would join her group in 2020 for a staff scientist position to lead the CIDC bioinformatic project.
I witnessed the development of many groundbreaking computational tools for genomics in Shirley’s lab. One tool that I found particularly elegant was BETA (Binding and Expression Target Analysis), developed by Su Wang and published in Nature Protocols in 2013.
My ChIP-seq data are 36bp single end reads. I usually use bowtie1 for mapping ChIP-seq reads, but bowtie1 does not handle indels. Since I want to call…
I am currently experimenting snakemake for pipelines. We will have paired samples when processing data. e.g. ChIP-seq (IP vs Input), DNA-seq (Normal vs…
When compare different ChIP-seq data sets or analyze a set of ChIP-seq data sets together (e.g. ChromHMM analysis), it is desirable to subsample the deeply…
I am experimenting DiffBind to do the same thing, which internally uses EdgR, DESeq and DESeq2. The author Rory Stark is very responsive on the bioconductor…
I am going to demonstrate how to make Upset plot using UpSetR package for ChIP-seq peaks. After running a peak-calling method for 3 samples, you want to…
I want to use MACS2 call ChIP-seq peaks for 10 samples(each with IP and input control) with 4 different set of parameters. That’s a lot of commands to type!…