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 ...
- 15.1k
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 ...
- 1,394
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 ...
- 4,202
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 ...
- 201
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
- 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.
- 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 ...
- 1,698
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 ...
- 216
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 ...
- 19.8k
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:
...
- 1,698
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.
- 19.8k
2
votes
Accepted
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 ...
- 4,721
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 ...
- 4,202
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 ...
- 141
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:
...
- 15.1k
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 ...
- 15.1k
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, ...
- 1,511
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__♦
- 13k
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__♦
- 13k
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
- 636
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.
- 2,061
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 ...
- 1,698
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 ...
- 3,341
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 ...
- 19.8k
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 ...
- 19.8k
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 ...
- 3,341
1
vote
Accepted
Peak-calling using homer
You just need to strip the / from $d, for which there are a number of options:
...
- 19.8k
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 ...
- 19.8k
1
vote
Only top scored, non community-wiki answers of a minimum length are eligible