ATAC seq enhancer help
Hello everyone,
I am analyzing ATAC-seq data to identify enhancers. This is my first time doing this particular analysis. I am using Bowtie2 to align the raw sequencing data. I used their default settings for paired-end reads. I have two questions:
- Does anyones know what the default distance is when classifying alignments as "concordant vs. discordant"?
- What the ATAC seq fragments sizes usually are with respect to enhancers? (to see if their default size setting is actually in line with what I want to see in this case)
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Ram
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mrs.whirly •
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mrs.whirly •
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1) It should be the default value of the
-Xparameter in bowtie2.2) No preference afaik. Enhancers have nucleosome-free regions and histone signals like many other open regions. I do not see how you could identify enhancers purely based on ATAC-seq. You would need functional data to demonstrate activating functions towards the target genes or at least ChIP-seq data for activating histone marks. Not every open and non-promoter region is an enhancer.