--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) |
--colorspace <Boolean> |
Use colorspace encoding (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: true) |
-d, --destination <ClcUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--downstream |
|
Integer: >= 0 |
Number of flanking downstream residues relative to the gene annotation to be used for mapping the reads (default: 0) |
--exon-discovery <Boolean> |
Exon discovery (default: true) |
--exon-discovery-min-coverage |
|
Double: 0.0 <= x <= 1.0 |
Minimum exon coverage fraction (default: 0.2) |
--exon-discovery-min-length |
|
Integer: >= 1 |
Minimum length of putative exons (default: 50) |
--exon-discovery-min-reads |
|
Integer: >= 0 |
Minimum number of reads (default: 10) |
--expression-level <String> |
Expression level possible values: Genes, Transcripts (default: Genes) |
--expression-value <String> |
Expression values possible values for "Genes" : RPKM, UNIQUE_GENE_COUNT, TOTAL_GENE_COUNT, UNIQUE_EXON_COUNT, TOTAL_EXON_COUNT, MEDIAN_COVERAGE and possible values for "Transcripts" : RPKM, UNIQUE_TRANSCRIPT_COUNT, TOTAL_TRANSCRIPT_COUNT (default: RPKM) |
-i, --input <ClcUrl> |
Input data on server |
--len-fraction |
|
Double: 0.0 <= x <= 1.0 |
Minimum fraction of read length that should align (applies to long reads) (default: 0.9) |
--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) |
--max-distance |
|
Integer: 0 <= x <= 50000 |
Maximum paired distance (default: 250) |
--min-distance |
|
Integer: 0 <= x <= 50000 |
Minimum paired distance (default: 180) |
--min-similarity |
|
Double: 0.0 <= x <= 1.0 |
Minimum fraction of similarity of read that should align (applies to long reads) (default: 0.8) |
--mismatch |
|
Integer: 0 <= x <= 3 |
Maximum number of mismatches allowed (applies to short reads) (default: 2) |
--organism <String> |
Organism type, possible values: Prokaryote, Eukaryote (default: Eukaryote) |
--reference <ClcUrl> |
Reference sequences |
--strand-specific <Boolean> |
Use strand specific assembly (default: false) |
--upstream |
|
Integer: >= 0 |
Number of flanking upstream residues relative to the gene annotation to be used for mapping the reads (default: 0) |
--use-annotations <Boolean> |
Use annotations for gene and transcript identification (default: true) |