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4 votes
Accepted

DESeq2 for large number of samples takes too much RAM

I'll preface this by saying that I don't think DESeq2 is the right tool to use for ATAC-Seq data. My own study of ATAC-Seq patterns [admittedly only a couple of runs that were our first exploration of ...
gringer's user avatar
  • 14.2k
3 votes
Accepted

ATAC peak anatations

ATAC-seq data is fundamentally different from RNA-seq data because they measure different things. RNA-seq data is typically mapped from raw sequencing reads to annotated gene transcripts. This has a ...
James Hawley's user avatar
  • 1,384
3 votes
Accepted

Loss and gain of region in ATAC seq

What you are looking for is "Differential accessibility analysis", you are using ATAC-seq, hence "accessibility". You will need to "call" and then "normalize" "count"(*) peaks, after these, you can ...
haci's user avatar
  • 4,132
3 votes

Where are .motif files from homer knownResults?

I have provided a solution in Biostars: If you edit the file findKnownMotifs.pl and move the call to printMotif to come before ...
malcook's user avatar
  • 191
3 votes
Accepted

How is PCR duplication rate computed in scATAC-seq?

The answer is in the supplementary methods page 3. Finally, all fragments in the same library with duplicate start and end coordinates were removed using Picard
GWW's user avatar
  • 752
2 votes
Accepted

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

Supplementary File 5 and 6 contain the code you're looking for.
menenuh's user avatar
  • 56
2 votes

ATAC seq peak annotation : Which peak to choose for downstream analysis

You can see from your table that the different peaks correspond to different promoters for different transcripts, for example, FAM41C has ENST00000432963.1, ENST00000446136.1, ENST00000635557.1. And ...
StupidWolf's user avatar
  • 1,688
2 votes

ATAC seq peak annotation : Which peak to choose for downstream analysis

I'll consider all peaks around promoter of particular gene as one peak. Moreover I'll interpret this as an open chromatin region = active gene. Why? Why there's no one wide peak which represents open ...
Adamm's user avatar
  • 206
2 votes
Accepted

GC normalization ATAC seq data

The only reason to normalize for GC content in RNA-seq is if it differs notably between samples/groups. If that's not the case and you aren't trying to compare genes withing samples then you have no ...
Devon Ryan's user avatar
  • 19.6k
2 votes
Accepted

Chromatin accessibility level on promoters with different CpG ratio calculation

Below I import the peaks call in narrowbed format from macs2 into a GRanges object. If you have a bed file, you can just use rtracklayer for it: ...
StupidWolf's user avatar
  • 1,688
2 votes
Accepted

Same region/region but different annotation

You have two different peaks at different positions with different annotations. This makes complete sense, you're just misreading it.
Devon Ryan's user avatar
  • 19.6k
2 votes
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Integrative analysis of omics studies using machine learning

The steps you describe are correct. For step 2 it is usually normalized to mean 0 and variance 1. However the "machine learning" part is important. Having several samples being technical replicates ...
llrs's user avatar
  • 4,713
2 votes

Integrate bulk RNA and ATAC-seq genes

If I am getting your question right, all you need is https://bioinfogp.cnb.csic.es/tools/venny/. I assume that your two lists corresponding to RNA-seq and ATAC-seq use the same set of gene identifiers ...
haci's user avatar
  • 4,132
2 votes

Error while running computeMatrix command in Deeptools

It worked, I installed a the newer version of deeptools, from GitHub: https://github.com/deeptools/deepTools
2 votes

How to identify genomic regions / peaks associated with enhancers (TF binding sites)? Is there a tool or a formal recipe?

If you have reads from chip-seq or atac you can use tools like homer or macs to identify peaks in your data. Once you have the peaks, these programs allow you to do motif discovery to annotate your ...
Niek de Klein's user avatar
2 votes

What is the required input peak file format for IDR (Irreproducible Discovery Rate)

As mentioned in the IDR readme on usage, there are examples in the IDR github repository here. Here's one of them: ...
gringer's user avatar
  • 14.2k
2 votes

Help with error DiffBind

I have very little idea what's going on here, but in the absence of any other answers or help, I'll try to work through this from a no-knowledge start point to see if I can hopefully help shift this ...
gringer's user avatar
  • 14.2k
2 votes

How to identify index sequences for cutadapt for atac-seq

The sequence to trim for ATAC-seq is CTGTCTCTTATACACATCT. It's the Nextera adapter sequence. The sequence is the reverse complement of the 3' ends of your primers, ...
ATpoint's user avatar
  • 1,326
1 vote
Accepted

Integrate bulk RNA and ATAC-seq genes

You requested I make a response. Okay, I'm reluctant to do this firstly, all my eukaryotes genomics is out of date except for immunology stuff and secondly, this is a hardcore eukaryote gene ...
M__'s user avatar
  • 12.5k
1 vote

DESeq2 for large number of samples takes too much RAM

Absolutely, look at Wilcox-rank, not purely because of the computational overhead, but the parametric assumption that DESeq2 uses are not correct on large data sets. This might describe your data ...
M__'s user avatar
  • 12.5k
1 vote
Accepted

How to extract DNA sequence from browser track input files (BigWig, bed etc.) files

[Here is the link.][1]. Instructions are very clear at the website [1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html
Supertech's user avatar
  • 606
1 vote

How to extract DNA sequence from browser track input files (BigWig, bed etc.) files

Bedtools can take a list of coordinates and a fasta and return a multifasta of the specified regions.
swbarnes2's user avatar
  • 1,921
1 vote
Accepted

ATAC seq density calculation

They are not referring to density of reads. It is the density of the fold change, the y variable in the plot to left of Fig2b. It tells you the distribution of the foldchange and 92% of the fold ...
StupidWolf's user avatar
  • 1,688
1 vote
Accepted

Getting two class of promoters : ATAC seq data

Its highly unlikely that you will be able to categorize promoters on this basis using only ATAC data. This is a consequence of people using the terms "promoters" and "transcription ...
Ian Sudbery's user avatar
  • 3,321
1 vote
Accepted

ATAC seq : Plotting insert sizes

You can exclude the which statement and get the entirety of all of the chromosomes. Note however that R is a very bad platform to use for this, since you end up ...
Devon Ryan's user avatar
  • 19.6k
1 vote
Accepted

Open chromatin region : nucleosome , mono-nucleosome , di-nucleosome

It's impossible to find nucleosome free and such regions without a BAM file. Your only options are: Filter the BAM files to contain only the size-range of interest and rerun the counting and ...
Devon Ryan's user avatar
  • 19.6k
1 vote
Accepted

ATAC-seq peak annotation and downstream analysis

The way we do this (and I think its quite common?), is to merge all the files of the same condition (taking the same number of reads from each), and then calling peaks on the merged sample - so you ...
Ian Sudbery's user avatar
  • 3,321
1 vote
Accepted

Peak-calling using homer

You just need to strip the / from $d, for which there are a number of options: ...
Devon Ryan's user avatar
  • 19.6k
1 vote
Accepted

Is it okay to use deeptools bamCompare (SES normalization) for comparisons across different ATAC-Seq datasets?

I would be very hesitant to use SES normalization in a case like this. We recommend that people run plotFingerprint first and see if there is good separation between the samples and only then using ...
Devon Ryan's user avatar
  • 19.6k
1 vote

ATAC-seq macs2 peak splitting in sliding windows

...
The Unfun Cat's user avatar

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