Question1:
We constructed paired-end reads and mate-pair reads libraries and performed DNA-seq of those libraries.
We constructed a whole genome assembly sequence by Platanus assembler using reads information from those libraries.
When using PSMC, is these a problem with using paired-end reads that constructed the whole genome assembly sequence. Or, if I map paired-end reads using gDNA from other individuals to the whole genome assembly sequence, is there a problem in the PSMC analysis?
Question2:
When using a genome assembly sequence with gDNA information of two individuals as a referecence, is it possible to use PSMC by polishing the sequence for one individual with a tool such as Pilon and using it a reference?
Hi developer
Question1: We constructed paired-end reads and mate-pair reads libraries and performed DNA-seq of those libraries. We constructed a whole genome assembly sequence by Platanus assembler using reads information from those libraries. When using PSMC, is these a problem with using paired-end reads that constructed the whole genome assembly sequence. Or, if I map paired-end reads using gDNA from other individuals to the whole genome assembly sequence, is there a problem in the PSMC analysis?
Question2: When using a genome assembly sequence with gDNA information of two individuals as a referecence, is it possible to use PSMC by polishing the sequence for one individual with a tool such as Pilon and using it a reference?
Best regards,