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I ran mosdepth twice on the same WES samples and got different coverage values. I used the same exome intervals bed file and reference genome build (hg38). There version of mosdepth used was different…
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Hello,
I ran kmc and kmc_tools with PacBio HiFi sequences of a diploid plant species:
kmc -m128 -k21 -t40 -ci1 -cs10000 xxx.hifi.fastq.gz xxx xxx_tmp
kmc_tools transform xxx histogram xxx.histo
…
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Hi,
I need to run TE-Aid in parallel but it causes errors because of using shared resources.
I tried this command (to copy TE-Aid to a temp file for each process so it doesn't use the same databa…
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Hi,
I tried to run your test_data, but I got this error:
```
########################################################
###### SV-HotSpot v1.0.0 ######
####################…
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Hi Matt,
Thanks for InStrain, it's a great piece of software! I'm no bioinformatician, but I've been trying to wrap my head around how the profile pipeline calculates breadth on a scaffold and geno…
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Dear @yinlabniu,
Thank you again for a very important tool to annotate CAZymes and identify CGCs in the microbial genomes of interest.
I am interested in examining how complete are the CGCs in my …
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See photo below, where high coverage gets cut-off (for alignment of _e.g.,_ R59_S11_L001_R2_001.fastq, R59_S11_L001_R1_001.fastq; hpv16_w12_ref.fasta). One way of getting around this is to log-scale t…
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Hi Glenn!
I'm currently running `cactus-hal2maf` on a new alignment I've generated using Cactus v2.8.2. I'm running Cactus as a singularity image on a computing cluster. Anyways, I have an alignmen…
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Hi, thanks for this fast and easy-to-run aligner :) I have two questions.
1. How the "coverage" in the report was calculated? I had a coverage value 0.95 from a human GRCh38 to human T2T alignme…
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I tried wit 700 Mbp genome and got a fantastic results! Thank you!!
Now I'm now working on a plant genome of ~4 Gbp and got segmentation fault problem.
So if it is using too much memory, is there …