diff options
Diffstat (limited to 'MANUAL.markdown')
| -rw-r--r-- | MANUAL.markdown | 23 |
1 files changed, 20 insertions, 3 deletions
diff --git a/MANUAL.markdown b/MANUAL.markdown index b802ab7..95438d6 100644 --- a/MANUAL.markdown +++ b/MANUAL.markdown @@ -400,7 +400,8 @@ instance, when seeking [structural variants]. The expected relative orientation of the mates is set using the [`--ff`], [`--fr`], or [`--rf`] options. The expected range of inter-mates distances (as measured from the furthest extremes of the mates; also called "outer distance") -is set with the [`-I`] and [`-X`] options. +is set with the [`-I`] and [`-X`] options. Note that setting [`-I`] and [`-X`] +far apart makes Bowtie 2 slower. See documentation for [`-I`] and [`-X`]. To declare that a pair aligns discordantly, Bowtie 2 requires that both mates align uniquely. This is a conservative threshold, but this is often desirable @@ -1520,7 +1521,15 @@ specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as [`-X`] is also satisfied). A 19-bp gap would not be valid in that case. If trimming options [`-3`] or [`-5`] are also used, the -[`-I`] constraint is applied with respect to the untrimmed mates. Default: 0. +[`-I`] constraint is applied with respect to the untrimmed mates. + +The larger the difference between [`-I`] and [`-X`], the slower Bowtie 2 will +run. This is because larger differences bewteen [`-I`] and [`-X`] require that +Bowtie 2 scan a larger window to determine if a concordant alignment exists. +For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very +efficient. + +Default: 0 (essentially imposing no minimum) </td></tr> <tr><td id="bowtie2-options-X"> @@ -1538,7 +1547,15 @@ proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as [`-I`] is also satisfied). A 61-bp gap would not be valid in that case. If trimming options [`-3`] or [`-5`] are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed -mates. Default: 500. +mates. + +The larger the difference between [`-I`] and [`-X`], the slower Bowtie 2 will +run. This is because larger differences bewteen [`-I`] and [`-X`] require that +Bowtie 2 scan a larger window to determine if a concordant alignment exists. +For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very +efficient. + +Default: 500. </td></tr> <tr><td id="bowtie2-options-fr"> |