Question: Assessing mapping quality from BAM files
gravatar for eurioste
5 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 • 478 views
ADD COMMENTlink modified 5 months ago by Hussain Ather860 • written 5 months ago by eurioste20

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

ADD REPLYlink written 5 months ago by genomax49k
gravatar for Hussain Ather
5 months ago by
Hussain Ather860
National Institutes of Health, Bethesda, MD
Hussain Ather860 wrote:

Check the quality control instructions here

ADD COMMENTlink written 5 months ago by Hussain Ather860
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