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Hello,
Firts of all, I would like to express my appreciation for the development of AA. I have been using AA extensively, and it has been a crucial tool in my research.
I am planning to use Hi…
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Hi all, I am working on benchmarking variant calling tools and I am now simulating low and high coverage hifi reads for this purpose. But I am not sure whether my workflow is correct as I received mes…
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Hello,
I have been trying to run goldrush with simulated HiFi reads of Human. The coverage of the reads is 10x. I have used goldrush for several other simulated inputs and it ran. I also checked if t…
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In https://ucsc-gi.slack.com/archives/CJ2EHEH1A/p1720038830195099?thread_ts=1719905671.084099&cid=CJ2EHEH1A, @benedictpaten notes that we could adjust out MAPQs to be "more confident" and "to the righ…
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Hi,
Thanks for developing this awesome tools. I'd like to get haplotype-specific HiFi reads via haplotype-specific kmers.
I run script to get haplotype-specific kmers, meryl version is 1.3:
`me…
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Hello All!
Im working with PacBio reads for the very first time. Compared to the tutorial, Im see im loosing really large number of reads. Below is the table:
Sample | ccs | primers | filtered…
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Hi,
Thanks for developing this tool.
I'd like to ask splitHaplotype is how to classify reads into different haplotypes.
My run script is:
`canu-2.2/bin/splitHaplotype -cl 1000 -memory 48 -thre…
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Hi Arang,
My assembly was constructed with HiFi reads only, and I try to use Merqury to evaluate my assembly, but the error I have encountered:
```shell
/nfs_fs/nfs3/jiezhang/sunwu_genome/softwar…
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Any idea of compatibility or performance with Pacbio HiFi reads?
Best
André
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Hi,
I tried to run your workflow on a dataset that was maybe a bit huge: 2x100Go of reads and 29Go of contigs.
The job fails with the following error message:
```
2024-09-13 03:37:18 bigben Sem…