Assessing mapping quality from BAM files

Question

[eurioste]

I have obtained multiple bam files mapped with BWA. I wish to asses if the mapping of my reads was successful and will give me useful data for a ChIP-seq experiment. Because this is a pilot experiment, I have no technical duplicates, just the input and one file for each ChIP protein/histone modification.

I'm new to NGS and this is my first time with ChiP-seq data. I wish to have an overview about how the reads are distributed across the genome and about how the mapping qualities are distributed. I also wish to know about any additional measures I should look in this case to asses the usefulness of my data.

Do you know which Galaxy main tools I could use to make plots and get this overview about the data? Tutorials and additional hints are welcome.

[GenoMax]

If you are limited to Galaxy tools then this would not help but otherwise check out Qualimap.

Answer 1

[Hussain Ather]

Check the quality control instructions here http://jvanheld.github.io/cisreg_course/chip-seq/practical/chip-seq.html