question-mark
Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Questions on PlotAggregate

See original GitHub issue

Hello, msbentsen, I have some questions when using TOBIAS for my ATAC-seq data analysis, I read the docs on TOBIAS Github, but still confused. My atac-seq analysis propose is finding different TFBS motifs of A549 cell line between conditionA and conditionB; And my analysis route like:

  • after alignment, i use macs2 for peak calling and got conditionA.narrowpeak and conditionB.narrowpeak(they are whole open site of each conditon);
  • then performed diff-peak analysis, then got peaks of unique open region of each condition, uniq_open_in_A.bed and uniq_open_in_B.bed(they are sub-set of conditionA.narrowpeak and conditionB.narrowpeak);
  • then use homer for motif enrichment on those unique open regions, and got interested motifs of each condition; till here, i got diff chromatin open regions uniq_open_in_A.bed and uniq_open_in_B.bed and motif on those region;

Next, I use TOBIAS for TF footprint analysis; after ATACorrect --> ScoreBigwig --> BINDetect --> PlotAggregate, I got my results, seems not the expected one(no obviously footprint on the aggregate plot on most enriched motif). Here are my aggregate plots: image compare to your example pic, it’s quite a different: image

Also, I made an aggregate plot between uncorrected and corrected, still not expected(the curve shape of uncorrected and corrected are very same, just one position higher than another on the Y-axis). Here’s the pic: image

I tried for couple of days, still cannot get a good plot on each condition.

So I will ask some question based on the information above:

  1. The result of scorebigwig(footprint.bw) and bindetect(TFBS.bed files) fit my expected result. But why aggregate-plot won’t show a ‘good-shaped’ footprint plot? If aggregate-plot is not good, can I still rely on footprint.bw and TFBS.bed files?
  2. I have conditionA and B .narrowpaek for the whole peak of two conditions, also uniq_open_A and B .bed for unique open regions(a subset of the whole peak), which kind of peak should I use in:
    • ATACorrect --peaks
    • ScoreBigwig --regions
    • BINDetect --peaks I tried both(whole peak and unique open peak), but cannot get a ‘good’ aggregate plot
  3. In aggregate plot: the plot curve between corrected.bw and uncorrected.bw, why their shape is so same, and just different position on Y-axis(not like figures in TOBIAS paper and GitHub), does this mean my correction won’t work? Please see pics above; My ATACorrect code is
TOBIAS ATACorrect \
    --bam conditionA.bam \
    --genome $hg38_path \
    --peaks uniq_open_A.bed \
    --blacklist $blacklist_path \
    --outdir ATACorrect_out \
    --cores 20
  1. When plotting aggregate footprint, I try to use --smooth 3 or 5, with this param, I can get a ‘better’ footprint plot, does this try make sense? Here is the smoothed pic: image

  2. in PlotAggregate method, What is the difference between these two arguments: --regions and --whitelist

Hope you can give me some advice, thanks.

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:10 (5 by maintainers)

github_iconTop GitHub Comments

1reaction
msbentsencommented, May 11, 2021

Great, I’m glad we got it solved in the end! I’m closing this issue but feel free to open another in case of other questions.

1reaction
hero-outmancommented, May 8, 2021

Hi msbentsen:

I think you are right, it’s my hg38 issue. I changed hg38.fa and performed ATACorrect again, got the clearly Tn5 motif. image

Thank you so much for the patience help, and may the force be with you!

Best Chu

Read more comments on GitHub >

github_iconTop Results From Across the Web

Solved Using the table below, graph the following aggregate
Question : Using the table below, graph the following aggregate supply and demand curves and then answer three questions and graph an AD...
Read more >
How to aggregate data and plot all groups - Stack Overflow
I want to visualize the average sales by types of Customer ( Segment ). I calculated the average sales by segment with this...
Read more >
Zoom fit for an aggregated dot plot - Questions
Hi - I am trying to set up a dot plot that aggregates samples means collected from the group. I can make the...
Read more >
Data Aggregation in Tableau
You can aggregate measures using Tableau only for relational data sources. ... To answer this question, you need to create a view that...
Read more >
Plot aggregated variable across two categorical variables
I think this question is more suited for stackoverflow. – DaSim · Thanks, I'll ask it there after the 90 minute post limit...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found