Workflow: pcr-bottleneck-coef.cwl

Fetched 2019-05-20 22:42:24 GMT

ChIP-seq - map - PCR Bottleneck Coefficients

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Inputs

ID Type Title Doc
input_bam_files File[]
input_output_filenames String[]
genome_sizes File

Steps

ID Runs Label Doc
bedtools_genomecov
bedtools-genomecov.cwl (CommandLineTool)

Tool: bedtools genomecov (aka genomeCoverageBed) Version: v2.25.0 Summary: Compute the coverage of a feature file among a genome.

Usage: bedtools genomecov [OPTIONS] -i <bed/gff/vcf> -g <genome>

Options: -ibam The input file is in BAM format. Note: BAM _must_ be sorted by position

-d Report the depth at each genome position (with one-based coordinates). Default behavior is to report a histogram.

-dz Report the depth at each genome position (with zero-based coordinates). Reports only non-zero positions. Default behavior is to report a histogram.

-bg Report depth in BedGraph format. For details, see: genome.ucsc.edu/goldenPath/help/bedgraph.html

-bga Report depth in BedGraph format, as above (-bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: \"grep -w 0$\" to the output.

-split Treat \"split\" BAM or BED12 entries as distinct BED intervals. when computing coverage. For BAM files, this uses the CIGAR \"N\" and \"D\" 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).

-strand Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6). - (STRING): can be + or -

-5 Calculate coverage of 5\" positions (instead of entire interval).

-3 Calculate coverage of 3\" positions (instead of entire interval).

-max Combine all positions with a depth >= max into a single bin in the histogram. Irrelevant for -d and -bedGraph - (INTEGER)

-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. - (FLOAT)

-trackline Adds a UCSC/Genome-Browser track line definition in the first line of the output. - See here for more details about track line definition: http://genome.ucsc.edu/goldenPath/help/bedgraph.html - NOTE: When adding a trackline definition, the output BedGraph can be easily uploaded to the Genome Browser as a custom track, BUT CAN NOT be converted into a BigWig file (w/o removing the first line).

-trackopts Writes additional track line definition parameters in the first line. - Example: -trackopts 'name=\"My Track\" visibility=2 color=255,30,30' Note the use of single-quotes if you have spaces in your parameters. - (TEXT)

Notes: (1) The genome file should tab delimited and structured as follows: <chromName><TAB><chromSize>

For example, Human (hg19): chr1 249250621 chr2 243199373 ... chr18_gl000207_random 4262

(2) The input BED (-i) file must be grouped by chromosome. A simple \"sort -k 1,1 <BED> > <BED>.sorted\" will suffice.

(3) The input BAM (-ibam) file must be sorted by position. A \"samtools sort <BAM>\" should suffice.

Tips: One can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ \"select chrom, size from hg19.chromInfo\" > hg19.genome

compute_pbc
compute-pbc.cwl (CommandLineTool)

Compute PCR Bottleneck Coeficient from BedGraph file.

Outputs

ID Type Label Doc
pbc_file File[]
Permalink: https://w3id.org/cwl/view/git/c269cecf317c699d6f3a0f44782e90914bce62b5/v1.0/map/pcr-bottleneck-coef.cwl