--auto-detect-paired-distances <Boolean> |
Determine appropriate paired distance limits automatically by sampling each paired read list. (default: true) |
--broken-pair-countingscheme <Boolean> |
When selected, both intact AND broken pairs are counted as two. When not selected, only intact pairs are counted and they are counted as one. Single reads are always counted as one. (default: false) |
--create-fusion-table <Boolean> |
Create fusion gene table (default: false) |
--create-fusion-table-min-reads |
|
Integer: 1 <= x <= 1000 |
Minimum read count fusion gene table (default: 5) |
--create-report <Boolean> |
Create report (default: true) |
--create-unmapped <Boolean> |
Create list of unmapped reads (default: false) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--deletion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a deletion (1, 2, or 3) (default: 3) |
--expression-value <[TPM, RPKM, UNIQUE_COUNTS, TOTAL_COUNTS]> |
Expression value (default: TOTAL_COUNTS) |
--genes <ClcObjectUrl> |
Select gene track |
--global-alignment <Boolean> |
When selected, end gaps are treated as mismatches. Otherwise, end gaps have no cost. (default: false) |
-i, --input <ClcObjectUrl> |
Input data on server |
--insertion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating an insertion (1, 2, or 3) (default: 3) |
--length-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum length fraction of a read that must match the reference sequence (default: 0.8) |
--limit |
|
Integer: 1 <= x <= 30 |
Reads that match in more positions than the specified number will be discarded (default: 10) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--mismatch-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a mismatch (1, 2, or 3) (default: 2) |
--mrna <ClcObjectUrl> |
Select mRNA track |
--reference <ClcObjectUrl> |
Reference sequences or sequence track |
--reference-type <[GENOME_ANNOTATED_WITH_GENES_AND_TRANSCRIPTS, GENOME_ANNOTATED_ONLY_WITH_GENES, ONE_REFERENCE_PER_TRANSCRIPT]> |
Select the type of reference used. Either (1) A reference genome, a gene and an mRNA track ('eukaryote' settings), (2) A reference genome and gene track ('prokaryote' settings) or (3) a list of ESTs (default: GENOME_ANNOTATED_WITH_GENES_AND_TRANSCRIPTS) |
--rpkm-without-transcripts <Boolean> |
For genes with no corresponding transcripts, create a single-exon transcript for the full gene body, and calculate expression for this as for any other transcript. (default: false) |
--similarity-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum fraction of similarity between read and reference sequence (default: 0.8) |
--spike-in-settings <[NONE, SPIKE_IN]> |
Map reads to spike-in controls (default: NONE) |
--spikein-controls <ClcObjectUrl> |
Select spike-in controls |
--strand <[BOTH_STRANDS, FORWARD, REVERSE]> |
Strand used by the mapper (default: BOTH_STRANDS) |
