Question: ATACseqQC - Cut-site probability greater than 1?
1
gravatar for ldyer2006
9 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 • 439 views
ADD COMMENTlink modified 15 days ago by Lizzy0 • written 9 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 9 months ago by genomax59k

Thanks a lot, that is very helpful.

ADD REPLYlink written 9 months ago by ldyer200630

can you post the graph?

ADD REPLYlink written 9 months ago by Friederike2.3k

How did you input you bam files using ATACseqQC? I used this commands in R: setwd("~/Documents/ATAC-Seq") where is the folder of my bam files, and the: bamfile <- "Test_ATAC-seq.bam", test <- readBamFile(bamfile, bigFile = TRUE). I checked the test and it always reported 0 sequences. While there are reads in my bamfile, it seemed that my bam file was not read in, could you please show me how to input my bam files? Thanks a lot.

ADD REPLYlink written 15 days ago by Lizzy0
1
gravatar for jianhong.ou
8 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 8 months ago by jianhong.ou10
1
gravatar for haibol2017
8 months ago by
haibol201710
haibol201710 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 8 months ago by haibol201710
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1573 users visited in the last hour