Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE algorithm. Any suggestion

Question

[Manhezz]

Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE algorithm. Any suggestion

[jared.andrews07]

What isn't clear? It's a pretty simple program to run. Feed in your peaks/BAMs and that's pretty much it. Note that the built-in annotations are ancient and you may be better served by building your own to feed in.

[Manhezz]

Thanks for the feedback I have installed the ROSE algorithm and I do not understand clearly what the option means when having ATAC-seq data.

ROSE_main.py [options] -g [GENOME] -i [INPUT_REGION_GFF] -r [RANKBY_BAM_FILE] -o [OUTPUT_FOLDER] [OPTIONAL_FLAGS]

could you elaborate on how to get the [INPUT_REGION_GFF]

[jared.andrews07]

That parameter is for peak regions. If you have a BED file of peaks, you can convert it to gff via bedops easily enough. Or use awk. That conversion has been answered many times on biostars.

Also, it's not really clear from your question whether you have H3K27ac or not, but if you do, I'd recommend that over ATAC-seq for SE calling.

[Manhezz]

$ python2.7 ROSE_main.py -g /home/hes/Desktop/data/hg18_refseq.ucsc -i /home/hes/Desktop/data/HG18_MM1S_MED1.gff -r /home/hes/Desktop/data/MM1S_MED1.hg18.bwt.sorted.bam -c /home/hes/Desktop/data/MM1S_WCE.hg18.bwt.sorted.bam -o Hez -s 12500 -t 2500.

On calling ROSE using the above code i encountered the error below yet i have the ROSE code in one directory.

python: can't open file '/ROSE_bamToGFF.py': [Errno 2] No such file or directory

[jared.andrews07]

I can't see your local file structure or where you downloaded ROSE from. Run ls from the directory and post the results along with wherever you downloaded the ROSE source code from (there are many clones of it floating around at this point, some with changes).

Also, hg18 is crazy old at this point, I'd recommend updating to newer genome builds if possible.

[Manhezz]

(ROSE) hesborn@hes-Latitude-5430:~/Desktop/ROSE$ ls
Hezz  LICENSE  patch.sh  README.md  ROSE_bamToGFF.py  ROSE_bamToGFF_turbo.py  ROSE_callSuper.R  ROSE_geneMapper.py  ROSE_main.py  ROSE_main_turbo.py  ROSE_utils.py  ROSE_utils.pyc

i git cloned ROSE from (https://github.com/Barski-lab/ROSE) i wanted to rerun the initial dataset from which ROSE Was built on, i changed to hg38 and try it on my dataset but i get the error below

(ROSE) hesborn@hesborn-Latitude-5430:~/Desktop/ROSE$ python ROSE_main.py -g /home/hesborn/Desktop/data/hg18_refseq.ucsc -i /home/hesborn/Desktop/data/HG18_MM1S_MED1.gff -r /home/hesborn/Desktop/data/MM1S_MED1.hg18.bwt.sorted.bam -c /home/hesborn/Desktop/data/MM1S_WCE.hg18.bwt.sorted.bam -o Hezz -s 12500 -t 2500




USING /home/hesborn/Desktop/data/HG18_MM1S_MED1.gff AS THE INPUT GFF
USING /home/hesborn/Desktop/data/hg18_refseq.ucsc AS THE GENOME
MAKING START DICT
LOADING IN GFF REGIONS
CHECKING INPUT TO MAKE SURE EACH REGION HAS A UNIQUE IDENTIFIER
REFERENCE COLLECTION PASSES QC
STITCHING REGIONS TOGETHER
PERFORMING REGION STITCHING
REMOVED 7865 LOCI BECAUSE THEY WERE CONTAINED BY A TSS
REMOVED 16 STITCHED LOCI BECAUSE THEY OVERLAPPED MULTIPLE TSSs
ADDED BACK 42 ORIGINAL LOCI
MAKING GFF FROM STITCHED COLLECTION
WRITING STITCHED GFF TO DISK AS Hezz/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff
OUTPUT WILL BE WRITTEN TO  Hezz/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_ENHANCER_REGION_MAP.txt
python /ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b /home/hesborn/Desktop/data/MM1S_MED1.hg18.bwt.sorted.bam -i Hezz/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff -o Hezz/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff &
python /ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b /home/hesborn/Desktop/data/MM1S_MED1.hg18.bwt.sorted.bam -i /home/hesborn/Desktop/data/HG18_MM1S_MED1.gff -o Hezz/mappedGFF/HG18_MM1S_MED1_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff &
python /ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b /home/hesborn/Desktop/data/MM1S_WCE.hg18.bwt.sorted.bam -i Hezz/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff -o Hezz/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_WCE.hg18.bwt.sorted.bam_MAPPED.gff &
python /ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b /home/hesborn/Desktop/data/MM1S_WCE.hg18.bwt.sorted.bam -i /home/hesborn/Desktop/data/HG18_MM1S_MED1.gff -o Hezz/mappedGFF/HG18_MM1S_MED1_MM1S_WCE.hg18.bwt.sorted.bam_MAPPED.gff &
PAUSING TO MAP






python: can't open file '/ROSE_bamToGFF.py': [Errno 2] No such file or directory
python: can't open file '/ROSE_bamToGFF.py': [Errno 2] No such file or directory
python: can't open file '/ROSE_bamToGFF.py': [Errno 2] No such file or directory
python: can't open file '/ROSE_bamToGFF.py': [Errno 2] No such file or directory
WAITING FOR MAPPING TO COMPLETE. ELAPSED TIME (MIN):
0

[jared.andrews07]

Well, that fork has made changes to the code. I don't know if it results in actual functional software or not. I kind of suspect not given some of the changes they've made. I'd go back to the original implementation.

[GenoMax]

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