.\" Man page generated from reStructuredText. . .TH "OBIJOINPAIREDEND" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obijoinpairedend \- description of obijoinpairedend . .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\%obijoinpairedend\fP aims at joining the two reads of a paired\-end library. .sp For this purpose, it concatenates sequence merging the forward read and the reversed\-complemented reverse read. .sp The program uses as input one or two sequences reads files. .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 If two files are used one of them must be specified using the \fB\-r\fP option. Sequence records corresponding to the same read pair must be in the same order in the two files. .IP \(bu 2 If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read. .UNINDENT .sp \fIExample:\fP .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obijoinpairedend \-r seq3P.fastq seq5P.fastq > seq.fastq .ft P .fi .UNINDENT .UNINDENT .sp The \fBseq5P.fastq\fP sequence file contains the forward sequence records. The \fBseq3P.fastq\fP sequence file contains the reverse sequence records. Pairs of reads are joined together and the resulting sequence is stored in the \(ga\(ga seq.fastq\(ga\(ga file. .UNINDENT .UNINDENT .SH OBIJOINPAIREDEND SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-r , \-\-reverse\-reads= Filename points to the file containing the reverse reads. .UNINDENT .SH OPTIONS TO SPECIFY INPUT FORMAT .SS Restrict the analysis to a sub\-part of the input file .INDENT 0.0 .TP .B \-\-skip The N first sequence records of the file are discarded from the analysis and not reported to the output file .UNINDENT .INDENT 0.0 .TP .B \-\-only Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the \fI–skip\fP option. .UNINDENT .SS Sequence annotated format .INDENT 0.0 .TP .B \-\-genbank Input file is in genbank format. .UNINDENT .INDENT 0.0 .TP .B \-\-embl Input file is in embl format. .UNINDENT .SS fasta related format .INDENT 0.0 .TP .B \-\-fasta Input file is in fasta format (including OBITools fasta extensions). .UNINDENT .SS fastq related format .INDENT 0.0 .TP .B \-\-sanger Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers). .UNINDENT .INDENT 0.0 .TP .B \-\-solexa Input file is in fastq format produced by Solexa (Ga IIx) sequencers. .UNINDENT .SS ecoPCR related format .INDENT 0.0 .TP .B \-\-ecopcr Input file is in ecoPCR format. .UNINDENT .INDENT 0.0 .TP .B \-\-ecopcrdb Input is an ecoPCR database. .UNINDENT .SS Specifying the sequence type .INDENT 0.0 .TP .B \-\-nuc Input file contains nucleic sequences. .UNINDENT .INDENT 0.0 .TP .B \-\-prot Input file contains protein sequences. .UNINDENT .SH OPTIONS TO SPECIFY OUTPUT FORMAT .SS Standard output format .INDENT 0.0 .TP .B \-\-fasta\-output Output sequences in \fBOBITools\fP fasta format .UNINDENT .INDENT 0.0 .TP .B \-\-fastq\-output Output sequences in Sanger fastq format .UNINDENT .SS Generating an ecoPCR database .INDENT 0.0 .TP .B \-\-ecopcrdb\-output= Creates an ecoPCR database from sequence records results .UNINDENT .SS Miscellaneous option .INDENT 0.0 .TP .B \-\-uppercase Print sequences in upper case (default is lower case) .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 AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .