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
| Flag | Arguments | Required | Description |
|---|---|---|---|
n/a | input | yes | The compact alignment file(s) to read as input. |
(-o|--output) | output | no | The basename of the output counts. |
(-g|--groups) | groups | no | Define 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 (/). |
--compare | compare | no | Compare 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-methods | normalization-methods | no | Comma 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) | stats | no | The filename where statistics will be written (for group comparisons). These files are tab delimited. Default value: comparison-stats.tsv |
(-w|--use-weights) | use-weights | no | Whether 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) | eval | no | Name 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- ;averages,t-test,fisher-r,BH |
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