Question: shift direction in ATAC/DNase data?
0
gravatar for star
3 months ago by
star70
Netherlands
star70 wrote:

I have two set of data about ATAC-seq and DNase-seq and I like to perform peak calling using MACS2, but I found that there are some differences in shift size (plus or minus direction). I like to know which one is better for either ATAC-seq or DNase-seq (e.g. --nomodel --shift -100 --extsize 200 or --nomodel --shift 100 --extsize 200). is it right that because most accessible regions in ATAC-seq and DNase-seq located in 5' region so using --shift -100 is recommended?

ADD COMMENTlink modified 3 months ago • written 3 months ago by star70
0
gravatar for ATpoint
3 months ago by
ATpoint11k
Germany
ATpoint11k wrote:

Just use --nomodel alone. If using no shifting model (from my understanding and experience), the use of shifting parameters does not make sense and does not change the output in comparison to using --nomodel alone.

For ATAC-seq (paired-end, deduplicated) I like:

macs2 callpeak -t in.bam -n name --keep-dup=all --nomodel -f BAMPE
ADD COMMENTlink modified 3 months ago • written 3 months ago by ATpoint11k

I am confused as to why so many papers use --shift -100 --extsize 200 for ATAC-seq data if this is not recommended for paired-end data? What is the reason for doing the shift and extsize?

ADD REPLYlink written 3 months ago by Lucy0

This has nothing to do with paired-end data. --nomodel deactivates the shifting model. Therefore, any shifting parameters do not make sense. I do not know why people use these settings, but it does not matter for the output. Try them out. You'll see (at least in my experience) that the number and location of the peaks will be the same. The use of BAMPE makes sense because in paired-end sequencing, one knows the true fragment sizes. When using BAM, macs estimates them, so BAMPE reduces the level of uncertainty.

ADD REPLYlink written 3 months ago by ATpoint11k

Thanks for your reply! is it necessary to use --nomodel for PE reads, I mean just use -f BAMPE. How about when there is SE reads, shall we use --nomodel --shift -100 --extsize 200?

ADD REPLYlink written 3 months ago by star70
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