...
| Code Block |
|---|
*****Required Options: BANDWIDTH=#integer# = Size of bandwidth for KDE calculation (default 3) CONVERSION=#character from#>#character to# #character from# = Character representing the modified ribonucleotide (default 'T') #character to# = Character representing what the modified ribonucleotide is read as by rTranscriptase (default 'C') note: only 1 conversion is possible at this time; in the future we may implement the ability to have 2 modified ribonucleotides MINIMUM_READ_COUNT_PER_GROUP=#integer# = Minimum number of reads required to call a group (default 10) MINIMUM_READ_COUNT_PER_CLUSTER=#integer# = Minimum number of reads required to call a cluster (default 1) MINIMUM_READ_COUNT_FOR_KDE=#integer# = Minimum read depth at a location to make a KDE estimate (default 1) => (recommended: 5) MINIMUM_CLUSTER_SIZE=#integer# = Minimum length required for a cluster to be reported (default 1) MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=#integer# = Minimum number of separate locations to have a reported conversion for a cluster to be reported (default 1) => (recommended: 2) note: setting this to 0 will cause errors, if you are looking for sites that may have no conversions, I recommended analyzing the 'groups' output file (see below) MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=#integer# = Minimum number of conversion events within a region to report a cluster (default 1) note: setting this to 0 will cause errors, if you are looking for sites that may have no conversions, I recommended analyzing the 'groups' output file (see below) MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=#integer# = Minimum read depth for a location to be included within a cluster (default 1) MINIMUM_READ_LENGTH=#integer# = Minimum length of mapped read to be included in the analysis (default 1) MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=#integer# = Maximum number of non-conversion mismatches of a mapped read to be included in the analysis (default 5) BOWTIE_FILE=#filepath/filename# = Location and name of a bowtie output file to be analyzed note: there can be multiple BOWTIE alignment files used as input, just create a new line with a new 'BOWTIE_FILE=' parameter GENOME_2BIT_FILE=#filepath/filename# = Location of the UCSC .2bit file of the genome against which the reads were aligned OUTPUT_CLUSTERS_FILE=#filepath/filename# = Location and name of the resulting clusters file |
...