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cloverliang 08-26-2015 08:00 AM

ATAC-seq cutting frequency analysis
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Hi everyone!

I'm analyzing ATAC-seq data. But I got problems in observing nice peaks as shown in Fig. 1c. in Buenrostro 2013 nature method paper.

I have the following steps:
1. Map to hg19 with bowtie2 (-X 2000).
2. Remove reads with MAPQ < 10 and sort bam file using samtools.
3. Remove duplicates using picard tools. (60%~70% duplication rate)
4. Merge sorted bam of four replicates together.
5. Get cutting position for each fragment and visualize cutting frequency (per basepair) in IGV.

I got the attached figure in the same position as shown in Fig. 1c. The first track is GM12878_ATACseq_50k. Data ranges from 0 to 6. There are some peaks but the noise-signal ratio seems really high. The second track is from ENCODE U Washington GM12865. Data range from 0 to 16. I wonder if I did something wrong or further smoothing/normalizing steps are needed.

Thank you!!

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