Input files

Wiggle format file:

Wiggle format file should contain protein occupancy data. We suggest using DANPOS to calculate occupancy from sequencing reads. DANPOS will save the occupancy data in .wig files.

Click for help information about .wig format.

Bed format file (--bed3file_paths):

Bed format file always contains a set of genomic elements, including their location in the genome. To be used by the Profile function in DANPOS, each .bed file must contain at least the following columns:

(1) chr chromosome name

(2) start the start point of an element

(3) end the end point of an element

Click for more help information about .bed format.

Gene file (--genefile_paths)

we suggest to download gene set from the UCSC table browser. Each file must contain at least the following columns:

(1) name Gene name

(2) chrom chromosome name

(3) strand Strand, can be "+" or "-"

(4) txStart the start point of gene body, must be smaller than txEnd

(5) txEnd the end point of gene body, must be larger than txStart

(6) cdsStart the start point of coding DNA sequence, must be smaller than cdsEnd

(7) cdsEnd the end point of coding DNA sequence, must be larger than cdsStart

(8) exonCount exon number

(9) exonStarts the start point of each exon, must be smaller than the associated exonEnd

(10) exonEnds the end point of each exon, must be larger than the associated exonStart