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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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**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
4 weeks ago
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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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Incorporate mappability into bin filtering/correction
mjz1 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 …
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Hi. I am trying to format my seg file to run CNV analysis on chromosome X. I've tried leaving the "chromosome" column notation as "X" and converted "X" to 23, however both attempts were unsuccessful w…
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I am getting this output when I run command `python pybsaseq.py -i variants_output.tsv -o output_pybsa_17102024 -p F2 -b 10,10`
```
The support for Qt4 was deprecated in Matplotlib 3.3 and will b…