*_Gateway_.BED

[Former user]

In my output, we have 2 BED files with *_Gateway and the number of super enhancers differs from the super enhancer.txt.

What is this output file?

[Brian Abraham]

This is not a typical output of ROSE. The names of the output files come directly from the name of the input file.

The output files are described here:

) OUTPUT:

All file names begin with the root of INPUT_CONSTITUENT_GFF

OUTPUT_DIRECTORY/gff/ .gff: copied .gff file of INPUT_CONSTITUENT_GFF (chrom, name, [blank], start, end, [blank], [blank], strand, [blank], [blank], name) STITCHED.gff: regions created by stitching together INPUT_CONSTITUENT_GFF at STITCHING_DISTANCE (chrom, name, [blank], start, end, [blank], [blank], strand, [blank], [blank], name) Name is number of constituents stitched together followed by ID of leftmost constituent. OUTPUT_DIRECTORY/mappedGFF/ _MAPPED.gff: output of bamToGFF using each bam file containing densities of factor in each constituent (constituent ID, region tested, average read density in units of reads-per-million-mapped per bp of constituent) _STITCHED_MAPPED.gff: output of bamToGFF using each bam file containing densities of factor in each stitched enhancer (stitched enhancer ID, region tested, average read density in units of reads-per-million-mapped per bp of stitched enhancer) OUTPUT_DIRECTORY/ STITCHED_ENHANCER_REGION_MAP.txt: all densities from bamToGFF calculated in stitched enhancers (stitched enhancer ID, chromosome, stitched enhancer start, stitched enhancer end, number of constituents stitched, rank of RANKING_BAM signal, signal of RANKING_BAM) Signal of RANKING_BAM is density times length. _AllEnhancers.table.txt: Rankings and super status for each stitched enhancer (stitched enhancer ID, chromosome, stitched enhancer start, stitched enhancer end, number of constituents stitched, size of constituents that were stitched together, signal of RANKING_BAM, rank of RANKING_BAM, binary of super-enhancer (1) vs. typical (0)) Signal of RANKING_BAM is density times length. _SuperEnhancers.table.txt: Rankings and super status for super-enhancers (stitched enhancer ID, chromosome, stitched enhancer start, stitched enhancer end, number of constituents stitched, size of constituents that were stitched together, signal of RANKING_BAM, rank of RANKING_BAM, binary of super-enhancer (1) vs. typical (0)) Signal of RANKING_BAM is density times length. _Enhancers_withSuper.bed: .bed file to be loaded into the UCSC browser to visualize super-enhancers and typical enhancers. (chromosome, stitched enhancer start, stitched enhancer end, stitched enhancer ID, rank by RANKING_BAM signal) *_Plot_points.png: visualization of the ranks of super-enhancers and the two groups. Stitched enhancers are ranked by their RANKING_BAM signal and their ranks are along the X axis. Corresponding RANKING_BAM signal on the Y axis.