Question: ATACseqQC - Cut-site probability greater than 1?
1
gravatar for ldyer2006
6 months ago by
ldyer200630
ldyer200630 wrote:

Hi guys,

I was just wondering if anybody here had any experience working with the ATACseqQC R package?

The package seems to function well for me over all, and gives reasonable results when I apply it to the entire mouse genome (Using the following command):

sigs.Irx3.0 <- factorFootprints(bamfiles = "Day0.shifted.bam", pfm = pwm,
                                                genome = Mmusculus, index = "Day0.shifted.bam",
                                                min.score="95%", seqlev=paste0("chr", c(1:19, "X", "Y")),
                                                upstream=100,downstream=100)

The problem then comes when I try to examine an individual chromosome, say chr1:

sigs.Irx3.0 <- factorFootprints(bamfiles = "Day0.shifted.bam", pfm = pwm,
                                                genome = Mmusculus, index = "Day0.shifted.bam",
                                                min.score="95%", seqlev=paste0("chr1"),
                                                upstream=100,downstream=100)

The function still runs, however it produces a graph with many spikes of cut-site probability greater than 1. I'm assuming that this is erroneous. If it's not, I can't find any details on the package's page or FAQs which would help me to interpret a cut-site probability higher than 1.

The package is designed for use with humans, as I understand it. I wonder if that has anything to do with the incorrect calculation of the cut-site. If so, are there any known solutions to this issue?

atacseqqc atac-seq • 300 views
ADD COMMENTlink modified 5 months ago by haibol20170 • written 6 months ago by ldyer200630

Please use the formatting bar (especially the code option) to format parts of you post that contain code snippets. I've done it for you this time. Formatting bar

ADD REPLYlink written 6 months ago by genomax55k

Thanks a lot, that is very helpful.

ADD REPLYlink written 6 months ago by ldyer200630

can you post the graph?

ADD REPLYlink written 6 months ago by Friederike2.1k
1
gravatar for jianhong.ou
5 months ago by
jianhong.ou10
jianhong.ou10 wrote:

Hi, Thank you for trying ATACseqQC. I am the author of ATACseqQC. If the probability greater than 1, there are two reasons: 1. most of the reads located in only one strand. 2. the reads depth are too low. If you don't mind, could you send me the files then I can improve the function to avoid this errors.

Jianhong

ADD COMMENTlink written 5 months ago by jianhong.ou10
0
gravatar for haibol2017
5 months ago by
haibol20170
haibol20170 wrote:

I am co-author of ATACseqQC paper (https://www.ncbi.nlm.nih.gov/pubmed/29490630). I have used 25% of aligned, duplicate-removed BAM file for one human chromosome (chr 1) to demonstrate the robustness of footprint analysis using ATACseqQC. I did see very spiky plots, but not encounter cutting probability greater than 1. Would you mind to share your chromosome-specific BAM file with us so we can try to reproduce the error and fix the potential bugs? Thanks!!

ADD COMMENTlink written 5 months ago by haibol20170
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