Question: Interpreting ATAC-seq alignment results
gravatar for hara
20 months ago by
hara0 wrote:

I have two ATAC-seq data samples which I aligned to reference genome hg19 using STAR aligner. How do I judge the quality of the data? I am new to ATAC-sequencing and understanding the data quality. The mapping results are as below: **

  • Sample 1:

* Tags mapped %: 22.32 Multi-mapped reads %: 1.23 Mapped duplicates %: 5.44 Tags unmapped %: 71.01 *

  • Sample 2:

** Tags mapped %: 41.80 Multi-mapped reads %: 2.90 Mapped duplicates %: 13.43 Tags unmapped %: 41.88

genomics atac-seq • 751 views
ADD COMMENTlink written 20 months ago by hara0

Does your reference genome contain chrM? Based on the unmapped percentage, I bet it doesn't. Are these primary samples or cell lines and what protocol has been used to generate them?

ADD REPLYlink modified 20 months ago • written 20 months ago by ATpoint31k
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