I don’t understand the meaning of the two options “–maxExpected” and “–topPercent” in blast2rma very well. Could you please explain them in more detail? By the way, if I want to perform LCA with all alignments of each reads(contigs), should I set “topPercent” to 100?
Thank you in advance.
-maxExpected sets an upper threshold for the e-value of alignments.
-topPercent sets the percentage of bit score that a competing alignment must achieve to also be considered by the LCA. Setting this to 100% is not a good idea, as this will result in loss of specificity.