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Hello,
Thank you for the software--it seems very promising. I am having an issue with generating results, however, as the output file is always empty and the log only gives an error "WARNING: Reac…
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I liked your idea to write the invalid UMI reads to a separate file instead of doing nothing at all with them. I think I will utilize this in my script as well.
Your algorithm looks like it will c…
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Thank you for making and maintaining dnaapler!
Streptomyces and other genera have linear chromosomes and often also linear plasmids.
Multiple genes on these replicons are located in a conserved…
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When I used LoopEnhance, I got errors when dealing with some chromosome, but worked for other chromosomes. Besides, when I use the parameter "--small_matrix_size 64 --step_size 64" rather than "--smal…
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**1. What were you trying to do?**
I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly, I used `vg autoindex` to build index f…
zwh82 updated
3 weeks ago
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**CHM13V2 T2T Assembly**
```bash
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
snipe sketch --ref GCF_00…
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A tool frequently used in order to submit genomes to ENA requires that scaffolds be >2Gb
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I am plotting runs of homozygosity and am using plot_StackedRuns. Is there any way to get 1 plot with all chromosomes instead of separate plots for each chromosome?
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Hi, I have a question about hicMergeMatrixBins behavior and I would like to ask you for some clarification.
I use hicexplorer 3.7.5 working with h5 files.
I've noticed, that hicMergeMatrixBins c…
qolba updated
4 months ago
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In our experiment, we cross-linked chromosome fragments that may interact in three-dimensional space, basecalling with dorado and identifying methylation information. I need to split the cross-linked …