dyogenibens / regulus Goto Github PK

Hello,
So I did not know how to adress this question to you, and I thought here would be easier.
I downloaded the files containing the predictions for enhancers and their targets for the human and zebra fish genomes from your group's NAR paper.
In the paper you calculated a normalized linkage score going from 0 to 1, while in the CNE data file there's no column called linkage score but rather one called segregation.score. Does that represent the linkage score meaning the higher it is the more synteny you observe between the enhancer and the target gene? Related to that do you use any cutoff on the linkage score and/or the phyloP values?
Thanks a lot in advance for your time.

Hello,
I am trying to use the Regulus python scripts in order to generate lists of CNEs and their associated genes for all human chromosomes. When I attempt to use the scanmaf.py script (scanmaf.py chrX.maf.gz -w 10 -x 3 -i 90 -f 10 -t 88 -n 8 -l 80 > chrX.res) I get the following message:
IOError: [Errno 2] No such file or directory: '//SM_annot_avril12/vicPac1_annotation_exons.rr'
even though I have not selected -a or -r as options. Why does this occur?
Also, where does one find the remred.py script?
Thanks,
Madeline

Dear, teams

Recent, I have read your articles which published on nature communication (in 2015) and nucleic acids research (in 2020).

As you said in paper "Linking long distance regulatory regions to the genes they regulate is important to study and understand the function of enhancers. Three main categories of experimental methods have been developed to assign enhancers to target genes in a genome-wide manner. The use of methods based on evolutionary principles could solve these difficulties, because they do not depend on the specific biological contexts required by experimental assays and are more easily applicable to multiple species"

Regulus is a wonderful tools to predict the target genes of regulatory elements.

I want use your tools for my research. But, because I don't know exactly how many input files are generated, and what each row and column of the output results represent. So I can't make good use of the tools you developed.

If you can provide more detailed documentation, this may be more conducive to the use and development of software.

Thank you very much.
@DyogenIBENS @JosephLucas

Dear, teams

Recent, I have read your articles which published on nature communication (in 2015) and nucleic acids research (in 2020).

As you said in paper "Linking long distance regulatory regions to the genes they regulate is important to study and understand the function of enhancers. Three main categories of experimental methods have been developed to assign enhancers to target genes in a genome-wide manner. The use of methods based on evolutionary principles could solve these difficulties, because they do not depend on the specific biological contexts required by experimental assays and are more easily applicable to multiple species"

Regulus is a wonderful tools to predict the target genes of regulatory elements.

I want use your tools for my research. But, because I don't know exactly how many input files are generated, and what each row and column of the output results represent. So I can't make good use of the tools you developed.

If you can provide more detailed documentation, this may be more conducive to the use and development of software.

Would you mind share the steps for preparing input files for anyone.

Thank you very much.

@DyogenIBENS @JosephLucas @alouis72

Good day, .

I'm trying to use scanmaf on the Ensembl 95 16-species fish alignment located at:

ftp://ftp.ensembl.org/pub/release-95/maf/ensembl-compara/multiple_alignments/23_fish.epo/

I've tried using the default parameters with only 2 species to consider as a starting point, but I recieve the following error:

reading ./maf-files/16_fish.epo.8_1.maf.gz with W= 50 ID= 90 MAS= 300 X= 3 F= 0 T= 60 N= 6
considering the following 2 species ['amphiprion_percula', ' astatotilapia_calliptera']
Traceback (most recent call last):
File "./scanmaf.py", line 477, in
score=champs[1].split("=")

Any advice would be greatly appreciated. Thanks.