cai1991
cai1991
Hi, Robert, The coverage of my ont reads is ~66X. I mapped illumina reads to the assembled contigs to call variations with GATK. No reference for variation calling. The coverage...
We generated these ont reads from 3 flowcells. The mean.q are 9.4, 8.9 and 8.8. I merged these reads together to use. Best regards, Chengcheng
Thank you for the suggestion. I will try it. Best regards, Chengcheng
Hi, Robert, I suddenly realize that I used fasta files (both for the sequences and target sequences) for Racon polishing. And the overlaps file is in paf format and was...
I used smartdenovo to assemble raw ont reads. It produced very continuous contigs with contig N50 of 9.2Mb and total contig size of 550Mb. I was very satisfied with these...
I'm not sure about the details of how this assembler works. But from what I read on their github page, [https://github.com/ruanjue/smartdenovo/blob/master/README-tools.md](url) the final consensus sequence is more accurate than raw...
Dear Shujun, Sorry for the late response. I did not yet figure it out and was too occupied by other stuff. Another thing I would like to mention is that...
Yes, each time the same issue happens. Best, Chengcheng
Hi Shujun, I still have the issue (I can ensure that there is no other version of Repeatmasker masking the conda version). I also tried the latest version (v2.2.2) you...
Hi @oushujun , Sorry for the long delay. This is the issue caused by RepeatMasker (https://github.com/Dfam-consortium/RepeatMasker/issues/271). Best regards,