usage: An example usage is:$ bamCoverage -b reads.bam -o coverage.bw

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), and 1x depth (reads per genome coverage, RPGC). Required arguments: --bam BAM file, -b BAM file BAM file to process (default: None) Output: --outFileName FILENAME, -o FILENAME Output file name. (default: None) --outFileFormat {bigwig,bedgraph}, -of {bigwig,bedgraph} Output file type. Either \"bigwig\" or \"bedgraph\". (default: bigwig) Optional arguments: --help, -h show this help message and exit --scaleFactor SCALEFACTOR The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the –binSize is set to 20 and the –smoothLength is set to 60, then, for each bin, the average of the bin and its left and right neighbors is considered. Any value smaller than –binSize will be ignored and no smoothing will be applied. (default: 1.0) --MNase Determine nucleosome positions from MNase-seq data. Only 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. Only fragment lengthsbetween 130 - 200 bp are considered to avoid dinucleosomes or other artifacts.*NOTE*: Requires paired-end data. A bin size of 1 is recommended. (default: False) --filterRNAstrand {forward,reverse} Selects RNA-seq reads (single-end or paired-end) in the given strand. (default: None) --version show program's version number and exit --binSize INT bp, -bs INT bp Size of the bins, in bases, for the output of the bigwig/bedgraph file. (default: 50) --region CHR:START:END, -r CHR:START:END Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) --blackListFileName BED file, -bl BED file A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. (default: None) --numberOfProcessors INT, -p INT Number of processors to use. Type \"max/2\" to use half the maximum number of processors or \"max\" to use all available processors. (default: max/2) --verbose, -v Set to see processing messages. (default: False) Read coverage normalization options: --normalizeTo1x EFFECTIVE GENOME SIZE LENGTH Report read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC)). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. The scaling factor used is the inverse of the sequencing depth computed for the sample to match the 1x coverage. To use this option, the effective genome size has to be indicated after the option. The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Common values are: mm9: 2,150,570,000; hg19:2,451,960,000; dm3:121,400,000 and ce10:93,260,000. See Table 2 of http://www.plosone.org /article/info:doi/10.1371/journal.pone.0030377 or http ://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_ T1.html for several effective genome sizes. (default: None) --ignoreForNormalization IGNOREFORNORMALIZATION [IGNOREFORNORMALIZATION ...] A list of space-delimited chromosome names containing those chromosomes that should be excluded for computing the normalization. This is useful when considering samples with unequal coverage across chromosomes, like male samples. An usage examples is --ignoreForNormalization chrX chrM. (default: None) --skipNonCoveredRegions, --skipNAs This parameter determines if non-covered regions (regions without overlapping reads) in a BAM file should be skipped. The default is to treat those regions as having a value of zero. The decision to skip non-covered regions depends on the interpretation of the data. Non-covered regions may represent, for example, repetitive regions that should be skipped. (default: False) --smoothLength INT bp The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the --binSize is set to 20 and the --smoothLength is set to 60, then, for each bin, the average of the bin and its left and right neighbors is considered. Any value smaller than --binSize will be ignored and no smoothing will be applied. (default: None) Read processing options: --extendReads [INT bp], -e [INT bp] This parameter allows the extension of reads to fragment size. If set, each read is extended, without exception. *NOTE*: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. *Single- end*: Requires a user specified value for the final fragment length. Reads that already exceed this fragment length will not be extended. *Paired-end*: Reads with mates are always extended to match the fragment size defined by the two read mates. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. The input of a fragment length value is optional. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads). (default: False) --ignoreDuplicates If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate's position also has to coincide to ignore a read. (default: False) --minMappingQuality INT If set, only reads that have a mapping quality score of at least this are considered. (default: None) --centerReads By adding this option, reads are centered with respect to the fragment length. For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. (default: False) --samFlagInclude INT Include reads based on the SAM flag. For example, to get only reads that are the first mate, use a flag of 64. This is useful to count properly paired reads only once, as otherwise the second mate will be also considered for the coverage. (default: None) --samFlagExclude INT Exclude reads based on the SAM flag. For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand. (default: None)

usage: An example usage is:$ bamCoverage -b reads.bam -o coverage.bw

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), and 1x depth (reads per genome coverage, RPGC). Required arguments: --bam BAM file, -b BAM file BAM file to process (default: None) Output: --outFileName FILENAME, -o FILENAME Output file name. (default: None) --outFileFormat {bigwig,bedgraph}, -of {bigwig,bedgraph} Output file type. Either \"bigwig\" or \"bedgraph\". (default: bigwig) Optional arguments: --help, -h show this help message and exit --scaleFactor SCALEFACTOR The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the –binSize is set to 20 and the –smoothLength is set to 60, then, for each bin, the average of the bin and its left and right neighbors is considered. Any value smaller than –binSize will be ignored and no smoothing will be applied. (default: 1.0) --MNase Determine nucleosome positions from MNase-seq data. Only 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. Only fragment lengthsbetween 130 - 200 bp are considered to avoid dinucleosomes or other artifacts.*NOTE*: Requires paired-end data. A bin size of 1 is recommended. (default: False) --filterRNAstrand {forward,reverse} Selects RNA-seq reads (single-end or paired-end) in the given strand. (default: None) --version show program's version number and exit --binSize INT bp, -bs INT bp Size of the bins, in bases, for the output of the bigwig/bedgraph file. (default: 50) --region CHR:START:END, -r CHR:START:END Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) --blackListFileName BED file, -bl BED file A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. (default: None) --numberOfProcessors INT, -p INT Number of processors to use. Type \"max/2\" to use half the maximum number of processors or \"max\" to use all available processors. (default: max/2) --verbose, -v Set to see processing messages. (default: False) Read coverage normalization options: --normalizeTo1x EFFECTIVE GENOME SIZE LENGTH Report read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC)). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. The scaling factor used is the inverse of the sequencing depth computed for the sample to match the 1x coverage. To use this option, the effective genome size has to be indicated after the option. The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Common values are: mm9: 2,150,570,000; hg19:2,451,960,000; dm3:121,400,000 and ce10:93,260,000. See Table 2 of http://www.plosone.org /article/info:doi/10.1371/journal.pone.0030377 or http ://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_ T1.html for several effective genome sizes. (default: None) --ignoreForNormalization IGNOREFORNORMALIZATION [IGNOREFORNORMALIZATION ...] A list of space-delimited chromosome names containing those chromosomes that should be excluded for computing the normalization. This is useful when considering samples with unequal coverage across chromosomes, like male samples. An usage examples is --ignoreForNormalization chrX chrM. (default: None) --skipNonCoveredRegions, --skipNAs This parameter determines if non-covered regions (regions without overlapping reads) in a BAM file should be skipped. The default is to treat those regions as having a value of zero. The decision to skip non-covered regions depends on the interpretation of the data. Non-covered regions may represent, for example, repetitive regions that should be skipped. (default: False) --smoothLength INT bp The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the --binSize is set to 20 and the --smoothLength is set to 60, then, for each bin, the average of the bin and its left and right neighbors is considered. Any value smaller than --binSize will be ignored and no smoothing will be applied. (default: None) Read processing options: --extendReads [INT bp], -e [INT bp] This parameter allows the extension of reads to fragment size. If set, each read is extended, without exception. *NOTE*: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. *Single- end*: Requires a user specified value for the final fragment length. Reads that already exceed this fragment length will not be extended. *Paired-end*: Reads with mates are always extended to match the fragment size defined by the two read mates. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. The input of a fragment length value is optional. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads). (default: False) --ignoreDuplicates If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate's position also has to coincide to ignore a read. (default: False) --minMappingQuality INT If set, only reads that have a mapping quality score of at least this are considered. (default: None) --centerReads By adding this option, reads are centered with respect to the fragment length. For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. (default: False) --samFlagInclude INT Include reads based on the SAM flag. For example, to get only reads that are the first mate, use a flag of 64. This is useful to count properly paired reads only once, as otherwise the second mate will be also considered for the coverage. (default: None) --samFlagExclude INT Exclude reads based on the SAM flag. For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand. (default: None)

usage: An example usage is:$ bamCoverage -b reads.bam -o coverage.bw

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), and 1x depth (reads per genome coverage, RPGC). Required arguments: --bam BAM file, -b BAM file BAM file to process (default: None) Output: --outFileName FILENAME, -o FILENAME Output file name. (default: None) --outFileFormat {bigwig,bedgraph}, -of {bigwig,bedgraph} Output file type. Either \"bigwig\" or \"bedgraph\". (default: bigwig) Optional arguments: --help, -h show this help message and exit --scaleFactor SCALEFACTOR The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the –binSize is set to 20 and the –smoothLength is set to 60, then, for each bin, the average of the bin and its left and right neighbors is considered. Any value smaller than –binSize will be ignored and no smoothing will be applied. (default: 1.0) --MNase Determine nucleosome positions from MNase-seq data. Only 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. Only fragment lengthsbetween 130 - 200 bp are considered to avoid dinucleosomes or other artifacts.*NOTE*: Requires paired-end data. A bin size of 1 is recommended. (default: False) --filterRNAstrand {forward,reverse} Selects RNA-seq reads (single-end or paired-end) in the given strand. (default: None) --version show program's version number and exit --binSize INT bp, -bs INT bp Size of the bins, in bases, for the output of the bigwig/bedgraph file. (default: 50) --region CHR:START:END, -r CHR:START:END Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10 or --region chr10:456700:891000. (default: None) --blackListFileName BED file, -bl BED file A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. (default: None) --numberOfProcessors INT, -p INT Number of processors to use. Type \"max/2\" to use half the maximum number of processors or \"max\" to use all available processors. (default: max/2) --verbose, -v Set to see processing messages. (default: False) Read coverage normalization options: --normalizeTo1x EFFECTIVE GENOME SIZE LENGTH Report read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC)). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. The scaling factor used is the inverse of the sequencing depth computed for the sample to match the 1x coverage. To use this option, the effective genome size has to be indicated after the option. The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Common values are: mm9: 2,150,570,000; hg19:2,451,960,000; dm3:121,400,000 and ce10:93,260,000. See Table 2 of http://www.plosone.org /article/info:doi/10.1371/journal.pone.0030377 or http ://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_ T1.html for several effective genome sizes. (default: None) --ignoreForNormalization IGNOREFORNORMALIZATION [IGNOREFORNORMALIZATION ...] A list of space-delimited chromosome names containing those chromosomes that should be excluded for computing the normalization. This is useful when considering samples with unequal coverage across chromosomes, like male samples. An usage examples is --ignoreForNormalization chrX chrM. (default: None) --skipNonCoveredRegions, --skipNAs This parameter determines if non-covered regions (regions without overlapping reads) in a BAM file should be skipped. The default is to treat those regions as having a value of zero. The decision to skip non-covered regions depends on the interpretation of the data. Non-covered regions may represent, for example, repetitive regions that should be skipped. (default: False) --smoothLength INT bp The smooth length defines a window, larger than the binSize, to average the number of reads. For example, if the --binSize is set to 20 and the --smoothLength is set to 60, then, for each bin, the average of the bin and its left and right neighbors is considered. Any value smaller than --binSize will be ignored and no smoothing will be applied. (default: None) Read processing options: --extendReads [INT bp], -e [INT bp] This parameter allows the extension of reads to fragment size. If set, each read is extended, without exception. *NOTE*: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. *Single- end*: Requires a user specified value for the final fragment length. Reads that already exceed this fragment length will not be extended. *Paired-end*: Reads with mates are always extended to match the fragment size defined by the two read mates. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. The input of a fragment length value is optional. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads). (default: False) --ignoreDuplicates If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate's position also has to coincide to ignore a read. (default: False) --minMappingQuality INT If set, only reads that have a mapping quality score of at least this are considered. (default: None) --centerReads By adding this option, reads are centered with respect to the fragment length. For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. (default: False) --samFlagInclude INT Include reads based on the SAM flag. For example, to get only reads that are the first mate, use a flag of 64. This is useful to count properly paired reads only once, as otherwise the second mate will be also considered for the coverage. (default: None) --samFlagExclude INT Exclude reads based on the SAM flag. For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand. (default: None)