fanc aggregate data

Question

fanc aggregate data

shinohara-xiao opened this issue a year ago · 2 comments

HI, When I'm trying to run

fanc aggregate output/hic/binned/fanc_example_100kb.hic \
               architecture/domains/gm12878_tads.bed \
               architecture/aggregate/fanc_example_100kb.agg

I do not find the folder "output" in the folder "example", instead, I used the hic data from "architecture/other-hic/fanc_example.juicer.hic@100kb" , and I got an result as following,

which is pretty different from the result as shown in the docs where the data from 'output/hic/binned/fanc_example_100kb.hic' is used.

I wonder whether the result is correct and I did not change any other paremeters in my code,my code is as following:

fanc aggregate 
architecture/other-hic/fanc_example.juicer.hic@100kb 
architecture/domains/gm12878_tads.bed 
architecture/aggregate/fanc_example_100kb.agg 
-p architecture/aggregate/fanc_example_100kb.agg.png 
-m architecture/aggregate/fanc_example_100kb.agg.txt

Wishing for the answers and thank you very much .

Answer 1 · 2023-07-13T10:04:33.000Z

Hi,
The output/ folder will be created after running the example pipeline, hopefully my reply to your otehr question helps with getting this running.

Your code / output look comparable to the first example in the documentation here, to me (the change in diagonal orientation is due to a plotting difference between versions, I believe). The docs there provide a worked example of the impact of the various parameters to fanc aggregate, so probably by having a look at those you will find a parameter combination that gives you the output plot you're looking for! :)

Answer 2 · 2023-07-18T02:57:26.000Z

Hi,
Thanks for you answering and that helps me a lot. Here I have another question when I'm running fanc aggregate
Here is my code:

fanc aggregate  GSE63525_GM12878_insitu_combined.hic  \
                            ArrowHead_GM12878_primary+replicate.bed \
                            FANC/output/fanc_gm12878.agg \
                            FANC/output/fanc_gm12878.agg.png \
                            FANC/output/fanc_gm12878.agg.txt

the fanc_gm12878.agg.png is like this:

I'm afraid the result is not right.However, when I read the docs, I do not find any parameters that I can use to revise the result. And the picture after O/E and large is like this:

The hic file is from Genome Browser (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63525&format=file&file=GSE63525%5FGM12878%5Finsitu%5Fprimary%2Breplicate%5Fcombined%2Ehic)
The bed file is the tads found by ArrowHead, and the file is like this:

Do I did anything wrong? Or，is my file wrong ?

Sorry to bother, It would be very grateful if you could help me with this.
Looking forward to your answering.