QuEST Parameters for ATAC-Seq

[Liang]

Hi,

I have questions regarding QuEST parameter setting for ATAC-Seq and would appreciate your valuable suggestions.

Q1. There’s no input control file for ATAC-Seq, so I type my command line as the following. It could run, but do you think it’s correct?

~/Desktop/QuEST_2.4/generate_QuEST_parameters.pl -sam_align_ChIP ./ATAC-G5-01.sam -gt ./genome_table -ap ./QuEST_analysis -ChIP_name QuEST_ATAC-G5-t1

Q2. I have troubles to select parameters that suit ATAC-Seq and I am wondering if anyone has recommended parameters (ChIP enrichment, ChIP extension enrichment, and the value of peak shift) for ATAC-Seq. I highlight my selections in red.

 ----------- QuEST parameter configuration -------------

What kind of ChIP experiment is this?

1. Transcription factor with defined motif and narrow (punctate) binding site

   resulting in regions of enrichment 100-300 bp wide.

   (bandwidth = 30 bp, region_size = 300 bp)

2. PolII-like factor resulting in regions of enrichment 300-1000 bp with

   some narrow binding sites and some wide sites possibly occupying

   the entire gene length.

   (bandwidth = 60 bp, region_size = 600 bp)

3. Histone-type ChIP resulting in wide regions of enrichment

   1Kb and up possibly occupying multiple genes.

   (bandwidth = 100 bp, region_size = 1000 bp)

4. Neither, I would like to configure individual parametrs myself.

Please specify your selection [1-4]: 1

Let's now determine QuEST peak calling parameters.

(Parameters below are optimized for human and mouse data

when default stack collapsing is performed).

Choose one of the following options:

1. Stringent peak calling parameters.

   ChIP enrichment                 = 50

   ChIP to background enrichment   = NA

   ChIP extension enrichment       = 3

2. Recommended peak calling parameters.

   ChIP enrichment                 = 30

   ChIP to background enrichment   = NA

   ChIP extension enrichment       = 3

3. Relaxed peak calling parameters.

   ChIP enrichment                 = 10

   ChIP to background enrichment   = NA

   ChIP extension enrichment       = 3

4. Neither, I want to specify peak calling parameters myself.

Please specify your selection [1-4]: 4

Please specifty ChIP enrichment (1 or greater, recommended 30): 3

Please specify the ChIP extension enrichment (1 or greater, recommended 3): 2

The following parameters were specified for running QuEST:

positive_region_size               :  300

KDE_bandwidth                      :  30

ChIP_seeding_fold_enrchment        :  3

ChIP_extension_fold_enrichment     :  2

ChIP_to_background_fold_enrichment :  NA

Would you like to run QuEST analysis now? (y/n): y

.

.

.

peak shift mean: NA

peak shift median: NA

QuEST failed to identify regions to determine peak shift estimate.

Do you want to override the value of peak shift? (y/n): y

Please enter the value of peak shift (recommended 50): 50

---------------------------------------

Maybe the best way is to try and compare different parameters, but I think it would be much better if I could have your experience/suggestions first.

Thank you very much.

Best,

Liang

[Anton]

I posted the answer to a different thread. You can post there if you have more questions.

Thanks, Anton

https://groups.google.com/forum/#!topic/chipseq/dVf7SdDy8LE