Stack Exchange Network

Stack Exchange network consists of 174 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [atac-seq]

The tag has no usage guidance.

2
votes
1answer
73 views

Integrative analysis of omics studies using machine learning

I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow: Normalise samples, within each type of omics, from ...
0
votes
0answers
82 views

Using HOMER for differential ATACseq analysis

I am trying to understand how I can use HOMER for ATAC-seq paired-end experiments to first find similar peaks between replicates, then compare the combined output files in-between to find ...
-1
votes
1answer
63 views

DiffBind: Model must include count data for contrasts.

I am trying to use DiffBind for my ATACseq experiment going through the vignette for ...
0
votes
1answer
33 views

How is PCR duplication rate computed in scATAC-seq?

Reading Cusanovich et al. (2015) I encountered the sentence: We mixed pairs of cell lines (HEK293T or HL-60 versus GM12878), performed combinatorial cellular indexing, and sequenced the resulting ...
1
vote
0answers
16 views

ATACseq pipeline report generation issue

I am trying to run ATACseq pipeline: https://www.bioconductor.org/packages/release/bioc/html/esATAC.html On single end ATACseq...
-2
votes
1answer
39 views

Supplying adapter sequences for ATACseq pipeline

I have several atac_seq.gz files and I need to run the pipeline with them. I have single end ATACseq, so the function ...
-2
votes
1answer
33 views

rJava issue when trying to use ATACseq pipeline

I am trying to use the following ATACseq pipeline. Unfortunately when I am importing it with library(esATAC), it is giving me ...
2
votes
1answer
329 views

Normalize ATAC-seq/Dnase-seq sequencing reads coverage signals over estimated background

I'm trying to normalize the coverage signals of ATAC-seq reads against its own background using normal distribution, described in this paper It says: Finally, all open chromatin coverage ...
3
votes
2answers
220 views

Where are .motif files from homer knownResults?

I have been using homer's findMotifsGenome.pl, but with my new version (v4.9.1) of homer I don't get ...