.\" Man page generated from reStructuredText. . .TH "OLIGOTAG" "1" "Jan 28, 2019" " 1.02 12" "OBITools" .SH NAME oligotag \- description of oligotag . .nr rst2man-indent-level 0 . .de1 rstReportMargin \\$1 \\n[an-margin] level \\n[rst2man-indent-level] level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] - \\n[rst2man-indent0] \\n[rst2man-indent1] \\n[rst2man-indent2] .. .de1 INDENT .\" .rstReportMargin pre: . RS \\$1 . nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] . nr rst2man-indent-level +1 .\" .rstReportMargin post: .. .de UNINDENT . RE .\" indent \\n[an-margin] .\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] .nr rst2man-indent-level -1 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] .in \\n[rst2man-indent\\n[rst2man-indent-level]]u .. .sp \fI\%oligotag\fP designs a set of oligonucleotides that can be used for tagging a set of samples during PCR reactions, by adding the oligonucleotides on the 5’ end of the primers. Many options allow designing a set of oligonucleotides according to specified properties. .SH OLIGOTAG SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-L , \-\-oligo\-list= Filename containing a list of oligonucleotides. \fIoligotag\fP selects within this list the oligonucleotides that match the specified options. .sp \fBCAUTION:\fP .INDENT 7.0 .INDENT 3.5 Cannot be used with the \fB\-s\fP option. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-s ###, \-\-oligo\-size=### Size of oligonucleotides to be generated. .sp \fBCAUTION:\fP .INDENT 7.0 .INDENT 3.5 Cannot be used with the \fB\-L\fP option. .UNINDENT .UNINDENT .sp \fBWARNING:\fP .INDENT 7.0 .INDENT 3.5 A size equal or greater than eight often leads to a very long computing time and requires a large amount of memory. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-f ###, \-\-family\-size=### Minimal size of the oligonucleotide family to be generated. .UNINDENT .INDENT 0.0 .TP .B \-d ###, \-\-distance=### Minimal Hamming distance (number of differences) between two oligonucleotides. .UNINDENT .INDENT 0.0 .TP .B \-g ###, \-\-gc\-max=### Maximum number of G or C in the oligonucleotides. .UNINDENT .INDENT 0.0 .TP .B \-a , \-\-accepted= .INDENT 7.0 .INDENT 3.5 Selected oligonucleotides are constrained by the given pattern (only IUPAC symbols are allowed). .UNINDENT .UNINDENT .sp \fBCAUTION:\fP .INDENT 7.0 .INDENT 3.5 pattern length must have the same length as oligonucleotides. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-r , \-\-rejected= .INDENT 7.0 .INDENT 3.5 Selected oligonucleotides do not match the given pattern (only IUPAC symbols are allowed). .UNINDENT .UNINDENT .sp \fBCAUTION:\fP .INDENT 7.0 .INDENT 3.5 pattern length must have the same length as oligonucleotides. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-p ###, \-\-homopolymer=### Selected oligonucleotides do not contain any homopolymer longer than the specified length. .UNINDENT .INDENT 0.0 .TP .B \-P ###, \-\-homopolymer\-min=### Selected oligonucleotides contain at least one homopolymer longer or equal to the specified length. .UNINDENT .INDENT 0.0 .TP .B \-T , \-\-timeout= Timeout to identify a set of oligonucleotides of required size, as defined by the \fB\-f\fP option. .UNINDENT .SH COMMON OPTIONS .INDENT 0.0 .TP .B \-h, \-\-help Shows this help message and exits. .UNINDENT .INDENT 0.0 .TP .B \-\-DEBUG Sets logging in debug mode. .UNINDENT .SH EXAMPLES .INDENT 0.0 .INDENT 3.5 \fIExample 1:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > oligotag \-s 5 \-f 24 \-d 3 \-g 3 \-p 2 > mytags.txt .ft P .fi .UNINDENT .UNINDENT .sp Searches for a family of at least 24 oligonucleotides of a length of 5 nucleotides, with at least 3 differences among them, with a maximum of 3 C/G, and without homopolymers longer than 2. The resulting list of oligonucleotides is saved in the \fBmytags.txt\fP file. .UNINDENT .UNINDENT .sp \fIExample 2:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > oligotag \-d 5 \-L my_oligos.txt \-f 10 \-p 1 .ft P .fi .UNINDENT .UNINDENT .sp Searches for a subset of at least 10 oligonucleotides listed in the \fBmy_oligos.txt\fP file, with at least 5 differences among them, and without homopolymers. The \fBmy_oligos.txt\fP file must contain a set of oligonucleotides of the same length, with only one oligonucleotide per line. The resulting list of oligonucleotides is printed on the terminal window. .UNINDENT .UNINDENT .sp \fIExample 3:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > oligotag \-s 7 \-f 96 \-d 3 \-p 1 \-r cnnnnnn > mytags.txt .ft P .fi .UNINDENT .UNINDENT .sp Searches for a family of at least 96 oligonucleotides of a length of 7 nucleotides, with at least 3 differences among them, without homopolymers, and without a \fBC\fP in the first position. The resulting list is saved in the \fBmytags.txt\fP file. .UNINDENT .UNINDENT .sp \fIExample 4:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > oligotag \-s 9 \-f 24 \-d 3 \-a yryryryry > mytags.txt .ft P .fi .UNINDENT .UNINDENT .sp Searches for a family of at least 24 oligonucleotides of a length of 9 nucleotides, with at least 3 differences among them, and an alternation of pyrimidines and purines. The resulting list is saved in the \fBmytags.txt\fP file. Because of the constraints imposed by the \fB\-a\fP option, it is possible to compute longer oligonucleotides in a reasonable time. .UNINDENT .UNINDENT .UNINDENT .UNINDENT .SH REFERENCE .INDENT 0.0 .IP E. 3 Coissac. Oligotag: a program for designing sets of tags for next\-generation sequencing of multiplexed samples. Methods Mol Biol, 888:13\-31, 2012. .UNINDENT .SH AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .