Hello,
I am new to using Bowtie2 and am trying to understand the 'minimum score threshold' as it relates to sequence similarity. I will be using the 'local alignment mode' where the default minimum score threshold is 20 + 8.0 * ln(L). If I understand correctly by increasing the values in the formula, i.e. making it 20 + 10.0 * ln(L), I will get a higher alignment score which makes the minimum threshold more stringent. This value will change based on the read length of my sequences.
My question is, how do I adjust the formula to test for different sequence similarities? I.e I would like to know which sequences only hit at 99% sequence similarity or above, or 95 or 90, etc. I can't tell if the values given by the formula are on a scale, if they relate to something other than read length, or something else.
Thank you in advance
Damian
I am new to using Bowtie2 and am trying to understand the 'minimum score threshold' as it relates to sequence similarity. I will be using the 'local alignment mode' where the default minimum score threshold is 20 + 8.0 * ln(L). If I understand correctly by increasing the values in the formula, i.e. making it 20 + 10.0 * ln(L), I will get a higher alignment score which makes the minimum threshold more stringent. This value will change based on the read length of my sequences.
My question is, how do I adjust the formula to test for different sequence similarities? I.e I would like to know which sequences only hit at 99% sequence similarity or above, or 95 or 90, etc. I can't tell if the values given by the formula are on a scale, if they relate to something other than read length, or something else.
Thank you in advance
Damian
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