--auto-detect-paired-distances <Boolean> |
Determine appropriate paired distance limits automatically by sampling each paired read list. Applies to base-space mapping only. For color space alignment - or if deselected - the distance setting on paired read lists is used. (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) |
--color-error-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a color error (1, 2, or 3) (default: 3) |
--color-space <Boolean> |
Perform color space alignment for relevant data sets (default: true) |
--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 |
|
<[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) |
--mapping-type |
|
<[GENES_ONLY,WHOLE_GENOME]> |
Map reads to gene-region only or to full genome (default: GENES_ONLY) |
--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 (default: GENOME_ANNOTATED_WITH_GENES_AND_TRANSCRIPTS) |
--rpkm-without-transcripts <Boolean> |
For genes with no mRNA annotation calculate RPKM by using gene length for exon length (default: false) |
--similarity-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum fraction of similarity between read and reference sequence (default: 0.8) |
--strand |
|
<[BOTH_STRANDS, FORWARD,REVERSE]> |
Strand used by the mapper (default: BOTH_STRANDS) |