This mode converts goby compact alignments to counts for transcripts. It is implemented by edu.cornell.med.icb.goby.modes.CompactAlignmentToTranscriptCountsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe compact alignment file(s) to read as input.
(-o|--output)outputnoThe basename of the output counts.
(-g|--groups)groupsnoDefine groups for multi-group comparisons. The syntax of the groups arguments is id-1=basename1,basename2/id-2=basename4,basename5 Where id-1 is the id of the first group, defined to consist of samples basename1 and basename2. basename1 must refer to a basename provided as input on the command line (see input). Multiple groups are separated by forward slashes (/).
--comparecomparenoCompare transcript counts between groups of samples. The compare flag must be followed by group ids separated by slashes. For instance, if groups group-A and group-B have been defined (see --groups option), --compare group-A/group-B will evaluate statistical tests of different count representation between samples in groups A and B.
--normalization-methodsnormalization-methodsnoComma separated list of the normalization methods to apply. Method currently supported include (AC=aligned-count) normalization by aligned sample count, or (BUQ=bullard-upper-quartile) Bullard Upper Quantile normalization. By default both options are evaluated. This option is available since goby 1.5. Default value: aligned-count,bullard-upper-quartile
(-s|--stats)statsnoThe filename where statistics will be written (for group comparisons). These files are tab delimited. Default value: comparison-stats.tsv
(-w|--use-weights)use-weightsnoWhether weights should be used to adjust read counts. When the flag is true, this mode will try to load a weights file associated with each input basename (‘basename’.weight). If found, the weights are used to adjust the read count for annotations. This option is available since Goby 1.7. Default value: false
(-t|--eval)evalnoName the statistics to evaluate. The complete list of valid statistics names is "samples,fold-change,fold-change-magnitude,log2-fold-change,group-averages,t-test,fisher,fisher-r,chi-square,Bonferroni,BH". This option is available since Goby 1.7. Default value: samples,fold-change,fold-change-magnitude,log2-fold-change,group&#45
;averages,t-test,fisher-r,BH