Question: Assessing mapping quality from BAM files
gravatar for eurioste
11 months ago by
eurioste20 wrote:

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.

mapping chip-seq bam • 797 views
ADD COMMENTlink modified 11 months ago by Hussain Ather890 • written 11 months ago by eurioste20

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

ADD REPLYlink written 11 months ago by genomax59k
gravatar for Hussain Ather
11 months ago by
Hussain Ather890
National Institutes of Health, Bethesda, MD
Hussain Ather890 wrote:

Check the quality control instructions here

ADD COMMENTlink written 11 months ago by Hussain Ather890
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