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Hello,
I noticed that when different resolution used, the compartment results may change. Is there any standard to help decide an optimal value for binsize?
I attached some tests using differe…
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Phylogenetic analysis of genomes and metagenomes for the 1%.
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Is it possible to use SQuIRE with a non-model organism by providing the genome assembly in FASTA format and the Repeatmasker output files (.tab, .tsv) instead of running fetch? And which files and Rep…
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Hi!
I have used hifiasm(0.14-r312) on HiFi-reads only to assemble an allotetraploid plant(coverage ~50x). The options : -t48 -l0 were used in this assembly. All output files were generated successful…
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I try to use Clirc and I have a problem in the first step. When I try to extract circRNA sequences from my file with coordinates and reference genome that were used to detect circRNA i have the follow…
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Hello, we are keen to use MITE-Tracker on our insect genomes (size=300Mb, diploid genome). We tested the tool on a genome, expecting the run to be as short as the rice genome example of the BMC Bioinf…
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Total chromosome sizes are hardcoded in the function "macs2CallPeaksATACSeq" and "macs2CallPeaks" of ngstk.py. So I ran into problems when I did the analysis with mm9. Maybe this could be added to the…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): v1.2.9
- OS name and version (`lsb_release -ds`): Red Hat Enterprise Linux release 8.5 (Ootpa)
**To Reproduce**
Exact bcbio comma…
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Hi there! Thanks for the pipeline, it looks like exactly what I needed for my analysis.
Quick question - do I understand it correctly that if I have my reference genomes each in multiple contigs, …
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Here's a rough draft of a db schema for G2P associations (in normal form). Currently, it only handles univariate associations.
- David Heckerman, Christoph Lippert, Chris Widmer
Study id (unique g…