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Start Your TrialThis interface is used from the REST API to run the Cutadapt program. Our interface supports only uncompressed files at present. If you require an interface that supports compressed data, please let us know.
The Tool ID for this interface is CUTADAPT_XSEDE It is specified with tool=CUTADAPT_XSEDE
Supported parameters:
This tool is a little unusual. It requires the user to submit an intput file that is not going to be used.
input.infile_placeholder_ - This is a file that wont be used. It can be anything, A 2 byte file if you like. But it is required.
input.infile_notcompressed_ - Primary reads file. It will be named input.fastq
input.infile_compressed_ - Primary reads file name, it will be named input.fastq.gz
input.paired_endfilenotcompr_ - Paired end reads file (when paired ends =1) filename will be input2.fastq
input.paired_endfilecompr_ - Compressed Paired end reads file (when paired ends =1), filename will be input2.fastq.gz
vparam.runtime_ - Float - Maximum Hours to Run (up to 168 hours) default=0.5
vparam.num_cores_ - Integer - How many cores? Default =1, up to 24 allowed.
vapram.compressed_input_ - Switch - This specifies whether or not your input is compressed. Default =0
vparam.paired_ends_ - Switch - I have paired end reads. Default = 0
vparam.specify_3adapter_ - String Enter the 3' adapter. No default.
vparam.specify_3adapterpaired_ - String - Enter the 3' adapter -A for paired-end reads. Only when paired_end_=1.
vparam.specify_5adapter_ - String - Enter the 5' adapter No default.
vparam.specify_5adapterpaired_ - String - Enter the 5' adapter for paired end reads (-G) Only when $paired_ends_=1
vparam.specify_anywhichwayadapter_ - String - Enter an adapter that may be 3' or 5'
vparam.specify_anywhichwayadapterpaired_ - String - Enter an adapter that may be 3' or 5' for paired end reads (-B) Only when $paired_ends_=1
vparam.specify_maxerrorrate_ - Float - Maximum allowed error rate (-e, --error-rate). Default =0.1
vparam.only_mismatches_ - Switch - Allow only mismatches in alignments
vparam.specify_removenadapters_ - Integer - Remove up to COUNT adapters from each read (-n, --times)
vparam.overlap_minlength_ - Integer - Require MINLENGTH overlap between read and adapter (--overlap)
vparam.interpret_wildcards_ - Switch - Interpret IUPAC wildcards in reads
vparam.donot_interpretwildcards_ - Switch - Do not interpret IUPAC wildcards in adapters.
vparam.specify_adapterhandling_ - Excl - What to do with found adapters? trim, mask, lowercase, none default = trim
vparam.check_reversecomp_ - Switch - Check read AND reverse complement for adapter matches (not for paired end)
Additional read modifications
vparam.cut_length_ - Integer - Remove this many bases from each read (-u)
vparam.nextseq_trim_ - Integer - Number of nucleotides removed via NextSeq-specific quality trimming (each read; --nextseq-trim).
vparam.quality_cutoff_ - String - Trim low-quality bases from 5' and/or 3' ends -q ([5',]3prime). See manual for format.
vparam.quality_base_ - Integer - Assume that quality values in FASTQ are encoded as ascii (quality + N) default = 33
vparam.specify_length_ - Integer - Shorten reads to LENGTH (-l, --length)lied after adapter trimming.
vparam.specify_trimn_ - Switch Trim N's on ends of reads. (--trim-n)
vparam.specify_lengthtag_ - String - Search for TAG followed by a decimal number (--length-tag)
vparam.specify_stripsuffix_ - String - Remove this suffix from read names if present (--strip-suffix)
vparam.specify_addprefix_ - String - Add this prefix to read names (-x)
vparam.specify_addsuffix_ - String - Add this suffix to read names (-y)
vparam.specify_negtozero_ - Switch - Change negative quality values to zero (-z)
Filtering of processed reads
vparam.specify_discardlength_ - Integer - Discard reads shorter than LEN (-m; minimum)
vparam.specify_maxdiscardlength_ - Integer - Discard reads longer than LEN (-M; maximum)
vparam.specify_maxnbases_ - Integer - Discard reads with more than COUNT 'N' bases. (--max-n)
vparam.discard_maxerrs_ - Integer - Discard reads whose expected number of errors exceeds (--max-expected-errors)
vparam.discard_trimmed_ - Switch - Discard reads that contain an adapter (--discard-trimmed)
vparam.discard_untrimmed_ - Switch - Discard untrimmed reads (--discard-untrimmed)
vparam.discard_casava_ - Switch - Discard reads that did not pass CASAVA filtering (--discard-casava)\
Filtering of paired end reads
vparam.specify_paireddiscardlength_ - String - Discard paired end reads shorter than LEN (-m, --minimum-length LEN:LEN
vparam.specify_pairedmaxlength_ - String - Discard paired end reads longer than LEN (-M, --maximum-length LEN:LEN )
vparam.specify_pairedreadfilter_ Excl - Which reads in paired-end read have to match the filtering criterion (--discard-casava): any; both; first
Output options
vparam.specify_fullreport_ - Switch - Print full report (unchecked gives minimal)
vparam.specify_outputfile_ - String - Write trimmed reads to FILE named here (-o)
vparam.specify_pairedoutputfile_ - String - Write trimmed paired end reads to FILE named here (-p)
vparam.specify_fastaout_ -Switch - Output FASTA to standard output even on FASTQ input (--fasta)
vparam.specify_compression_ - Switch - Use compression level 1 for gzipped output files (-Z)
vparam.specify_infofile_ - String - Write information about each read and its adapter matches into FILE named here (--info-file)
vparam.specify_restfile_ - String - Write information about each read and its adapter matches into FILE named here (-r)
vparam.specify_tooshortfile_ - String - Write reads that are too short into FILE named here (--too-short-output)
vparam.specify_untooshortpairedreadoutfile_ - Switch - Write the second read in a pair to this file if pair is too short (--too-short-paired-output)
vparam.specify_toolongfile_ - String - Write reads that are too long into FILE named here (--too-long-output)
vparam.specify_toolongpairedreadoutfile_ -= Swtich - Write too long second reads to a file (--toolong-paired-output)
vparam.specify_untrimmedfile_ - String - Write reads that do not contain any adapter into FILE named here (--too-untrimmed-output)
vparam.specify_untrimmedpairedreadoutfile_ - Switch - Write paired reads that do not contain any adapter into a file (--untrimmed-paired-output)