This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. The coverage is calculated as the number of reads per bin, where bins are short consecutive counting windows of a defined size. It is possible to extended the length of the reads to better reflect the actual fragment length. bamCoverage offers normalization by scaling factor, Reads Per Kilobase per Million mapped reads (RPKM), counts per million (CPM), bins per million mapped reads (BPM) and 1x depth (reads per genome coverage, RPGC).
- Searches your data folder for the alignment file in .bam and .bam.bai format.
This capsule requires alignment files that are position sorted and indexed bam format. When you supply alignment files, the capsule will return normalized according to the features on App Panel selected.
In the case of one.
- bamFiles
- SampleA.bam
- SampleA.bam.bai
In the case of many.
- bamFiles
- SampleA.bam
- SampleA.bam.bai
- SampleB.bam
- SampleB.bam.bai
- SampleC.bam
- SampleC.bam.bai
Blacklist (if any)
- blacklist.bed
In your results folder you will find the bigWig file with normalizations applied.
In the case of one.
- Results
- SampleA.bw
In the case of many.
- Results
- SampleA.bw
- SampleB.bw
- SampleC.bw
- Number of Threads, if not utilized will automatically use all available.
- Bin Size.
- Any Chromosomes you wish to ignore during normalization. Default is chrX.
- Choose a Normalization Technique from the list of choices.
- Choose the version of genome your alignment file was generated from.
- Determinate nucleosome position (if MNase-Seq)
- Usage of Offset
- Emphasis on reads on the Forward or Reverse Strand.
- Region of the Genome to focus.
- Blacklisted Regions (if any)
- Exact scaling
- Skip Non Covered Regions
- Smooth length
- Extend Reads
- Ignore Duplicate Reads
- Center Reads
- Sam Field Include Flag
- Sam Field Exclude Flag
https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html