ch4rr0
commented
2 months ago Hello,
The L in L,0,-0.24 has nothing to do with local or end-to-end mode but is instead represents a (L)inear function used to calculate the minimum score a read must have to be considered a valid alignment, or the the number of Ns a read can possess to be considered for alignment. Both of these are calculated as a function of the read length. I hope this helps.
Setting function options
Some Bowtie 2 options specify a function rather than an individual number or setting. In these cases the user specifies three parameters: (a) a function type F, (b) a constant term B, and (c) a coefficient A. The available function types are constant (C), linear (L), square-root (S), and natural log (G). The parameters are specified as F,B,A - that is, the function type, the constant term, and the coefficient are separated by commas with no whitespace. The constant term and coefficient may be negative and/or floating-point numbers.
For example, if the function specification is L,-0.4,-0.6, then the function defined is:
f(x) = -0.4 + -0.6 * xIf the function specification is G,1,5.4, then the function defined is:
f(x) = 1.0 + 5.4 * ln(x)
Dear Bowtie2 developers,
This is the Bowtie2 code I run
bowtie2 --end-to-end --sensitive --score-min L,0,-0.24 -k 1 --n-ceil L,0,0.05 --threads $CPUS -x $GENOME_BOWTIE2_INDEX -U $READ_FILE.I have questions about this line of code: 1) do two letters of "L" next to "--score-min" and "--n-cell" mean local mode or seed length? I may be confused with the "-L" seed length option with just the letter "L".
2) if the "L" letters in the code mean local mode, then does this contradict the "--end-to-end" option? In this case, which option is going to override the other?
Regards,
Xiao