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I am running the latest release (2.2.3) on an ONT dataset that is mapped to GRCm39 using minimap2.
stringtie halts at the following bundle regardless how much memory space I allocate. I wonder if yo…
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This error appears to be similar to #1466
After running for a few weeks on ~50 mammalian fastas from NCBI, cactus crashes with two seemingly related errors from a bunch of toil jobs. I'm wondering…
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I performed buttery-eel basecalling on the slow5 file and got the fastq file. I want to detect m6A modification. Can I extract information from the slow5 file and the resulting fastq file to build a m…
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Hi!
When I use minimap2 in Geneious (minimap2_macos -x map-ont --frag=yes --secondary=no -a ref.fasta query.fasta -o output.sam) or with the command line (minimap2 -x map-ont --frag=yes --secondary=n…
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Hi,
I just switched minimap2 from 2.17 to 2.20, and now my syri plots (from same genome inputs) lose inversions, translocations and duplications. They also have more gaps, some of them where inversio…
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I have used purge_dups on various assemblies recently but have run into an issue where purge_dups dies partway through processing split.self.paf.gz with a segfault while using 4GB of ram. I have repli…
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Hi Im running the tool on 1 haplotype with a reference mode, using 240 GB and 32 Cores. I got this error.
[M::main] CMD: minimap2 -a -I 10G --eqx -x asm5 -t 4 --secondary=no /cbio/projects/031/moha…
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**I have read the paper (https://doi.org/10.1038/s41467-020-15171-6)
and the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about**
- align
- correct
- collapse
…
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**Describe the issue**
`bamtocov file.bam` generated "ERROR: coverage went backwards from 0 to 0"
**System information (please complete the following information):**
- UBUNTU 20.04 app
**Ad…
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Hi
I am trying RepeatFiller on multiple chain files for hg38->T2T and I am encountering some inconsistent errors.
The official chain file from T2T runs through without anything being reported - seem…