谢谢您。In de novo mode, the database is constructed on the fly using a strategy similar to Perseus: sequences are considered in the order of decreasing abundance, and candidate parents must have abundance at least 2× that of the query sequence, assuming chimeras are less abundant than their parents because they undergo fewer rounds of amplification. Sequences not classified as chimeric are added to the reference database.您好,再请教您一下,denovo模式是基于序列的丰富度进行考虑,因为在PCR扩增过程中,嵌合体是后面才开始形成的,所以嵌合体序列的丰富度比母体序列(非嵌合体序列)要少。那么,uchime的这个denovo模式是说对序列的丰富度进行分析,非嵌合体序列的丰度至少要是嵌合体序列的2倍才可以,是这样的理解吗
minh
The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.
xn
The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.
您好,这是mothur里chimera.uchime的两个参数,这两个参数的涵义可以给我讲一讲吗?谢谢您。
dereplicate
The dereplicate parameter can be used when checking for chimeras by group. If the dereplicate parameter is false, then if one group finds the sequence to be chimeric, then all groups find it to be chimeric, default=f. If you set dereplicate=t, and then run remove.seqs with dups=f you can remove only the redundant chimeric sequences.
我想请问您,mothur.uchime里的这个参数要怎么理解,默认值是F的意思是说:如果序列a在样品A是chimera,然后就认为所有样品(A/BC/D)里序列a都认为是chimera并把序列a移除吗?那么设dereplicate=t,又要怎么理解?我真是弄不清楚了,谢谢您了