Super enhancers

Question

[Oburah]

Hello,

I have ATAC-seq data (control and treatment), i am interested in calling enhancers and super-enhancer using this data. While i have executed ROSE algorithm from young`s lab on his dataset from chiq-seq. I am wondering if i can use ROSE on ATAC-SEQ and how can i confirm that the output from ROSE On ATAC-seq are SE/TE and not promoters??

[Oburah]

Thanks, I have called SE and TE using the ROSE algorithm as follows python2.7 ROSE_main.py -g HG38 -i /home/hesborn/Desktop/Data/S3vS2-2.gff -r /home/hesborn/Downloads/possorted_bam.bam -o Hezz -s 12500 -t 2500.

How can i look for binding motif and Transcription factors on the SE enhancers list generated?

[ATpoint]

Please don't ask unrelated questions in existing threads. Open a new question, indicating what you tried so far.

Answer 1

[jared.andrews07]

Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'll run fine.

ROSE excludes peaks within 2.5kb (I think) of the TSS from its stitching process. So while the resulting SEs may overlap promoters, there is some effort to avoid calling SEs that are driven pretty much solely by a promoter. ROSE also has some hidden logic/behavior where stitching will not occur if the stitched region spans the TSS of 3 or more genes. This causes gene-dense regions that look to have clear super enhancers by eye to be missed.

The annotations are also at least a decade old, and you have to alter the source code to provide new ones. Which I've found to be worth doing.

It's software that could really use some updates at this point, frankly.

[Oburah]

Hello, i encountered this problem when running ROSE, Do anyone know how to solve it?

python2.7 ROSE_main.py -g HG38 -i /home/hesborn/Desktop/Data/S3vS2-2.gff -r /home/hesborn/Downloads/possorted_bam.bam -o Hezz -s 12500 -t 2500



REMOVED 0 LOCI BECAUSE THEY WERE CONTAINED BY A TSS

REMOVED 0 STITCHED LOCI BECAUSE THEY OVERLAPPED MULTIPLE TSSs
ADDED BACK 0 ORIGINAL LOCI

MAKING GFF FROM STITCHED COLLECTION
WRITING STITCHED GFF TO DISK AS Hezz/gff/S3vS2-2_12KB_STITCHED_TSS_DISTAL.gff
OUTPUT WILL BE WRITTEN TO  Hezz/S3vS2-2_12KB_STITCHED_TSS_DISTAL_ENHANCER_REGION_MAP.txt
python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b /home/hesborn/Downloads/possorted_bam.bam -i Hezz/gff/S3vS2-2_12KB_STITCHED_TSS_DISTAL.gff -o Hezz/mappedGFF/S3vS2-2_12KB_STITCHED_TSS_DISTAL_possorted_bam.bam_MAPPED.gff &
python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b /home/hesborn/Downloads/possorted_bam.bam -i /home/hesborn/Desktop/Data/S3vS2-2.gff -o Hezz/mappedGFF/S3vS2-2_possorted_bam.bam_MAPPED.gff &
PAUSING TO MAP
{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'Hezz/mappedGFF/S3vS2-2_12KB_STITCHED_TSS_DISTAL_possorted_bam.bam_MAPPED.gff', 'bam': '/home/hesborn/Downloads/possorted_bam.bam', 'rpm': True, 'input': 'Hezz/gff/S3vS2-2_12KB_STITCHED_TSS_DISTAL.gff'}
[]
{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'Hezz/mappedGFF/S3vS2-2_possorted_bam.bam_MAPPED.gff', 'bam': '/home/hesborn/Downloads/possorted_bam.bam', 'rpm': True, 'input': '/home/hesborn/Desktop/Data/S3vS2-2.gff'}
[]
mapping to GFF and making a matrix with fixed bin number
mapping to GFF and making a matrix with fixed bin number
WAITING FOR MAPPING TO COMPLETE. ELAPSED TIME (MIN):
0
using a MMR value of 502.2775
using a MMR value of 502.2775
has chr
Number lines processed
has chr
Number lines processed
0
Traceback (most recent call last):
  File "ROSE_bamToGFF.py", line 247, in <module>
    main()
  File "ROSE_bamToGFF.py", line 238, in main
    newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix)
  File "ROSE_bamToGFF.py", line 74, in mapBamToGFF
    gffLocus = ROSE_utils.Locus(line[0],int(line[3]),int(line[4]),line[6],line[1])









IndexError: list index out of range

[jared.andrews07]

Based on the source code, it seems to be because the GFF record for that line is shorter than expected.

[Oburah]

Well-noted however just wondering what you me by GFF being shorter. Thank you

[jared.andrews07]

That is not valid GFF format, so that is probably going to be problematic. See the GFF spec for proper format.