DayTimeMouse

How to determine the quantity of various kinds of random mutations in a genomic simulation?

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Hi， I am quite puzzled about how to appropriately set the number of different types of mutations when simulating a human cancer genome. Could you provide me with some guidance...

Hi, I want to get both strands sequnces' kmer sets. Is right to add the -C parameter? Or, is it feasible to run jellyfish on forward and reverse complementary sequences...

Hi， Does bwa-mem2 have a function like --secondary=no? Just like minimap2. Best.

How to classify hifi reads into haplotype genomes? minimap2 did not work well

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Hi, I used HiFi + ONT + HiC reads to assemble haplotype genomes, then I want to classfiy hifi reads into haplotype genome separately. I have tried to use minimap2,...

Completeness, Switch Error？

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 Hi, What should the completeness in the picture be? Furthermore, what is the meaning of "all" ? Lastly, does the "2" mentioned in the picture refer to a Switch...

Hi, I want to ask how to set group counts in male? 23, 24(X and Y) or 25(X, Y and mitochondria)? Best wishes.

Hi, I use racon to polish the Scaffold (with N bases) after filling the gap. Will it work properly? I ran racon three rounds of error correction and got the...

How to get haplotype-specific reads?

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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: `meryl count...

version 1.7.0 run failed

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Hi, I installed deepsomatic 1.7.0(python 3.10.12), but run failed. The log is below: 2024-09-25 13:03:51.979669: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to...

Hi, Thanks for developing this awesome tools. I haver already used sv caller to call paired tumor and normal samples vcf file. Then, I'd like to use surviour to select...