Hi everybody,
We have recently done our first ATAC Seq project in our lab and my task is analysing the data. But since I am quite new to bioinformatics, I was wondering whether somebody here has experience with the different analysis steps?
So far, I've mapped the reads with bwt and have the .bam files.
Now in the paper (Buenrostro et al. 2013) they say they adjusted the read start sites to represent the center of the transposon binding event for peak calling and footprinting and then used ZINBA for peak calling.
How would I go about adjusting the read start sites?
And ZINBA wants .bed tagAlign or bowtie files. Would you simply transfom bam to bed with bedtools?
Thanks!
We have recently done our first ATAC Seq project in our lab and my task is analysing the data. But since I am quite new to bioinformatics, I was wondering whether somebody here has experience with the different analysis steps?
So far, I've mapped the reads with bwt and have the .bam files.
Now in the paper (Buenrostro et al. 2013) they say they adjusted the read start sites to represent the center of the transposon binding event for peak calling and footprinting and then used ZINBA for peak calling.
How would I go about adjusting the read start sites?
And ZINBA wants .bed tagAlign or bowtie files. Would you simply transfom bam to bed with bedtools?
Thanks!
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