Hello,dengfeng,
In the first step when I calculate the cutoff point in terms of coverage, the nanopore reads were compared to the assembled genome, but when I get to step 3 " purge_dups -2 -T cutoffs -c PB.base.cov asm.split.self.paf.gz > dups.bed 2> purge_dups.log " , there are no results in the bed file and the log file is as follows
Then I compared the assembled genome with Illumina reads in the first step, and the result was that the bed file still had no output until the third step, and the log file was the same as above.
Hope to receive your reply soon.
Best.
Hello,dengfeng, In the first step when I calculate the cutoff point in terms of coverage, the nanopore reads were compared to the assembled genome, but when I get to step 3 " purge_dups -2 -T cutoffs -c PB.base.cov asm.split.self.paf.gz > dups.bed 2> purge_dups.log " , there are no results in the bed file and the log file is as follows
[M::main] finish parsing params [M::main] finish reading hits [M::main] finish reading cutoffs [M::main] finish reading coverages [M::main] finish classifying sequences [M::main] finish filtering by tags [M::main] finish cleaning [M::main] finish sorting [M::main] finish indexing sequences [M::flt_by_bm_mm] check overpuring [M::main] finish reassigning sequences by bm and mm
Then I compared the assembled genome with Illumina reads in the first step, and the result was that the bed file still had no output until the third step, and the log file was the same as above. Hope to receive your reply soon. Best.