--adapters <String> |
Selected adapters, format: "Name: x,Sequence: x,Strand: [Plus|Minus],Action: [Discard when found|Discard when not found|Remove adapter], mismatch cost: x,gap cost: x,minimum score: x,minimum score end: x". Example: "Name: Illumina small RNA, Sequence: CAAGCAGAAGACGGCATACGA, Strand: Minus, Action: Discard when not found, mismatch cost: 3, gap cost: 5, minimum score: ns, minimum score end: 6" (default: ) |
--ambiguous-limit |
|
Integer: >= 0 |
Maximum number of ambiguous nucleotides allowed after trimming. Decreasing this value causes more stringent trimming (default: 2) |
--ambiguous-trim <Boolean> |
Trim ends based on the presence of ambiguity characters, e.g. N (default: true) |
--color-space <Boolean> |
Use colorspace (default: false) |
--create-report <Boolean> |
Create a report (default: true) |
-d, --destination <ClcUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--discard-long <Boolean> |
Discard long reads (default: false) |
--discard-long-limit |
|
Integer: >= 1 |
Discard all reads which consist of more residues than the given threshold (default: 1000) |
--discard-short <Boolean> |
Discard short reads (default: false) |
--discard-short-limit |
|
Integer: >= 0 |
Discard all reads which consist of less residues than the given threshold (default: 15) |
-i, --input <ClcUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--min-count |
|
Integer: >= 1 |
Minimum sampling count (internal use only) (default: 1) |
--quality-limit |
|
Double: 0.0 <= x <= 1.0 |
Decreasing this value causes more stringent trimming (default: 0.05) |
--quality-trim <Boolean> |
Trim ends using the prediction reliability calculated by the base-caller (default: true) |
--reverse-strand <Boolean> |
Will search on reversed complement sequence when linker(s) are not found on plus strand (default: false) |
--save-broken-pairs <Boolean> |
Create a sequence list containing reads from paired reads where one reads is completely trimmed (default: false) |
--save-discarded <Boolean> |
Create a sequence list containing the completely trimmed sequences (default: false) |