The workflow sample, described below, prepare ChIP-Seq processed data (with BedTools and bedGraphToBigWig) for visualization in a genome browser. For input BED-file produces BigWig file.
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.
The workflow sample "ChIP-Seq Coverage" can be found in the "NGS" section of the Workflow Designer samples.
The opened workflow looks as follows:
<center> <br> <img src="/wiki/download/attachments/13008919/Chip-Seq Coverage.png"/> <br> </center>
The wizard has 3 pages.
Input data Page: On this page you must input BED file with ChIP-Seq tags.
<center> <br> <img src="/wiki/download/attachments/13008919/Chip-Seq Coverage_1.png"/> <br> </center>
Parameters Page: Here you can optionally modify parameters that should be used for the Slopbed, Genome Coverage and BedGraphToBigWig elements.
<center> <br> <img src="/wiki/download/attachments/13008919/Chip-Seq Coverage_2.png"/> <br> </center>
The following parameters are available:
|Genome||In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. The format of the file is: (-g).|
|Each direction increase||Increase the BED/GFF/VCF entry by the same number base pairs in each direction. If this parameter is used -l and -l are ignored. Enter 0 to disable. (-b)|
|Substract from start||The number of base pairs to subtract from the start coordinate. Enter 0 to disable. (-l)|
Add to end
The number of base pairs to add to the end coordinate. Enter 0 to disable. (-r)
Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)
Define -l and -r as a fraction of the feature'Â€Â™s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp Â€ÂœupstreamÂ€Â. (-pct)
Print the header from the input file prior to results. (-header)
Filter start>end fields
|Remove lines with start postion greater than end position|
|Report mode||Histogram () - Compute a histogram of coverage. Per-base (0-based) (-dz) - Compute the depth of feature coverage for each base on each chromosome (0-based). Per-base (1-based) (-d) - Compute the depth of feature coverage for each base on each chromosome (1-based). BEDGRAPH (-bg) - Produces genome-wide coverage output in BEDGRAPH format. BEDGRAPH (including uncoveded) (-bga) - Produces genome-wide coverage output in BEDGRAPH format (including uncovered).|
|Split||Treat Â BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR Â and Â operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). (-split)|
|Strand||Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6). (-strand)|
|5 prime||Calculate coverage of 5'Â€Â™ positions (instead of entire interval). (-5)|
|3 prime||Calculate coverage of 3'Â€Â™ positions (instead of entire interval). (-3)|
|Max||Combine all positions with a depth >= max into a single bin in the histogram. (-max)|
|Scale||Scale the coverage by a constant factor.Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). Default is 1.0; i.e., unscaled. (-scale)|
|Trackline||Adds a UCSC/Genome-Browser track line definition in the first line of the output. (-trackline)|
|Trackopts||Writes additional track line definition parameters in the first line. (-trackopts)|
|Block size||Number of items to bundle in r-tree (-blockSize).|
|Items per slot||Number of data points bundled at lowest level (-itemsPerSlot).|
|Uncompressed||If set, do not use compression (-unc).|
Output Files Page: On this page you can select an output directory:
<center> <br> <img src="/wiki/download/attachments/13008919/Chip-Seq Coverage_3.png"/> <br> </center>