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Diffstat (limited to 'MANUAL.markdown')
| -rw-r--r-- | MANUAL.markdown | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/MANUAL.markdown b/MANUAL.markdown index 2ec2828..7378b1a 100644 --- a/MANUAL.markdown +++ b/MANUAL.markdown @@ -921,6 +921,46 @@ usually have extension `.fq` or `.fastq`. FASTQ is the default format. See also: [`--solexa-quals`] and [`--int-quals`]. </td></tr> +<tr><td id="bowtie2-options-interleaved"> + +[`--interleaved`]: #bowtie2-options-interleaved + + --interleaved + +</td><td> + +Reads interleaved FASTQ files where the first two records (8 lines) +represent a mate pair. + +</td></tr> +<tr><td id="bowtie2-options-tab5"> + +[`--tab5`]: #bowtie2-options-tab5 + + --tab5 + +</td><td> + +Each read or pair is on a single line. An unpaired read line is +[name]\t[seq]\t[qual]\n. A paired-end read line is +[name]\t[seq1]\t[qual1]\t[seq2]\t[qual2]\n. An input file can be a +mix of unpaired and paired-end reads and Bowtie 2 recognizes each +according to the number of fields, handling each as it should. + +</td></tr> +<tr><td id="bowtie2-options-tab6"> + +[`--tab6`]: #bowtie2-options-tab6 + + --tab6 + +</td><td> + +Similar to [`--tab5`] except, for paired-end reads, the second end can have a +different name from the first: +[name1]\t[seq1]\t[qual1]\t[name2]\t[seq2]\t[qual2]\n + +</td></tr> <tr><td id="bowtie2-options-qseq"> [`--qseq`]: #bowtie2-options-qseq |