ChIP-seq analysis ( QC)

Question

[mikysyc2016]

Before align to genome(bowtie), do you do quality cutoff? which software you used?

[ATpoint]

I use skewer to trim fastq files for a trailing base quality of 30, and an average base quality of the read of 25. Use fastqc to get an idea of the low-level data quality.

Answer 1

[Ankit]

You can also use Trimmomatic, if you have Illumina sequencing reads. I keep SLIDINGWINDOW:4:15 MINLEN:36. You can visualize after trimming by FastQC.