Difference between revisions of "Shore methyl"
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'''shore methyl''' | '''shore methyl''' | ||
quantifies methylated and unmethylated cytosines from BS-seq alignments (only [[genomemapper]]). | quantifies methylated and unmethylated cytosines from BS-seq alignments (only [[genomemapper]]). | ||
| + | |||
| + | ==Command line options== | ||
| + | |||
| + | '''Usage:''' shore methyl [OPTIONS] | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | | colspan=2 | '''Mandatory''' | ||
| + | |---- | ||
| + | | ''-n'' STRING || || Name (any of species, strain, accession, project or any other ID) | ||
| + | |---- | ||
| + | | ''-f'' STRING || || Reference genome sequence from the [[IndexFolder]], *.shore file | ||
| + | |---- | ||
| + | | ''-o'' STRING || || AnalysisFolder, will be created | ||
| + | |---- | ||
| + | | ''-i'' STRING[,...] || || [[shore directory|Shore directories]] or [[map.list]] file(s) | ||
| + | |---- | ||
| + | | ''-g'' INT || || Core offset - do not trust the first and last -g positions of the alignment. default: max MM's | ||
| + | Short read alignments are prone to misalignments towards the ends of the read. This value specifies how many bases at each end will be regarded as suspicious. | ||
| + | |---- | ||
| + | |---- | ||
| + | | colspan=2 | '''Quality threshold''' | ||
| + | |---- | ||
| + | | ''-q'' INT || (Default: ''5'') || Cutoff for base masking using Sanger calibrated qualities | ||
| + | |---- | ||
| + | | ''-c'' INT || || Cutoff for base masking using chastity values | ||
| + | |---- | ||
| + | |---- | ||
| + | | colspan=2 | '''Basecalling (scoring matrix approach)''' | ||
| + | |---- | ||
| + | | ''-a'' STRING || || Scoring matrix file (recommended, activates new basecalling approach) | ||
| + | |---- | ||
| + | | ''-b'' FLOAT || (Default: ''0.2'') || Minimum allele frequency of alternative base call | ||
| + | |---- | ||
| + | |---- | ||
| + | | colspan=2 | '''Basecalling (decision tree approach)''' | ||
| + | |---- | ||
| + | | ''-x'' INT || (Default: ''3'') || Minimum coverage threshold | ||
| + | |---- | ||
| + | | ''-m'' INT || (Default: ''3'') || Maximum observed to expected coverage | ||
| + | |---- | ||
| + | | ''-e'' FLOAT || (Default: ''0.1'') || Minimum observed to expected coverage | ||
| + | |---- | ||
| + | | ''-y'' FLOAT || (Default: ''0.8'') || Minimum concordance of homozygous SNPs (0 to 1) | ||
| + | |---- | ||
| + | | ''-d'' FLOAT || (Default: ''0.67'') || Minimum concordance of homozygous Indels | ||
| + | |---- | ||
| + | | ''-t'' FLOAT || (Default: ''0.25'') || Minimum frequency for heterozygous pos (0 to 1) | ||
| + | |---- | ||
| + | | ''-u'' FLOAT || (Default: ''0.02'') || Minimum frequency for minor allele pos (0 to 1) | ||
| + | |---- | ||
| + | | ''-z'' INT || (Default: ''10'') || Quality threshold, max base quality | ||
| + | |---- | ||
| + | |---- | ||
| + | | colspan=2 | '''Optional''' | ||
| + | |---- | ||
| + | | ''-v'' || || Create additional output files containing all intermediate data | ||
| + | |---- | ||
| + | | ''-r'' || || Graphical output of statistics using R | ||
| + | |---- | ||
| + | |---- | ||
| + | |} | ||
Latest revision as of 10:30, 28 September 2011
shore methyl quantifies methylated and unmethylated cytosines from BS-seq alignments (only genomemapper).
Command line options
Usage: shore methyl [OPTIONS]
| Mandatory | ||
| -n STRING | Name (any of species, strain, accession, project or any other ID) | |
| -f STRING | Reference genome sequence from the IndexFolder, *.shore file | |
| -o STRING | AnalysisFolder, will be created | |
| -i STRING[,...] | Shore directories or map.list file(s) | |
| -g INT | Core offset - do not trust the first and last -g positions of the alignment. default: max MM's
Short read alignments are prone to misalignments towards the ends of the read. This value specifies how many bases at each end will be regarded as suspicious. | |
| Quality threshold | ||
| -q INT | (Default: 5) | Cutoff for base masking using Sanger calibrated qualities |
| -c INT | Cutoff for base masking using chastity values | |
| Basecalling (scoring matrix approach) | ||
| -a STRING | Scoring matrix file (recommended, activates new basecalling approach) | |
| -b FLOAT | (Default: 0.2) | Minimum allele frequency of alternative base call |
| Basecalling (decision tree approach) | ||
| -x INT | (Default: 3) | Minimum coverage threshold |
| -m INT | (Default: 3) | Maximum observed to expected coverage |
| -e FLOAT | (Default: 0.1) | Minimum observed to expected coverage |
| -y FLOAT | (Default: 0.8) | Minimum concordance of homozygous SNPs (0 to 1) |
| -d FLOAT | (Default: 0.67) | Minimum concordance of homozygous Indels |
| -t FLOAT | (Default: 0.25) | Minimum frequency for heterozygous pos (0 to 1) |
| -u FLOAT | (Default: 0.02) | Minimum frequency for minor allele pos (0 to 1) |
| -z INT | (Default: 10) | Quality threshold, max base quality |
| Optional | ||
| -v | Create additional output files containing all intermediate data | |
| -r | Graphical output of statistics using R | |
