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I have been trying to run EarlGrey on my plant genome. Its a chromosome level assembly of 332Mb. The fasta file consists of 42 sequences with largest chromosome being 65Mb. The smallest sequences in t…
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Dear,
I'm trying to use the Capture function in Oligo to design probes against the mouse genome mm10. I'm using the following code:
`python design.py Capture -f GRCm38.primary_assembly.genome.…
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Hi,
I've followed the install instructions and am running a test on my dataset.
I am running with the following command:
```python3 mcclintock.py -r Iterative_pangenome_reveal_map_min10kb_u…
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Hello,
I got the following error:
The command was:
bedtools intersect -a /mnt/nvme0n1p1/ifengel/ChimeraTE/projects/chimera_test/tmp/TE_file.bed -wa -nonamecheck -b /mnt/nvme0n1p1/ifengel/C…
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Hi,
I use this pipeline to create genome alignment file with local mode. Here is my script
`make_chains.py human macAss hg38.2bit macAss.2bit --project_dir human_macAss --executor_queuesize 40`
…
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Hello,
Thanks for your work on this package!
I have been having issues trying to use EarlGrey as a non-root user on my university compute cluster. I followed the instructions under **Earl Grey In…
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Hello Robert,
Hope all is well. Thank you for developing RepeatMasker!
I installed RepeatMasker via conda. I commonly encounter such a scenario: when annotating genomes with RepeatMasker, the ex…
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Hello, Shujun!
I successfully ran EDTA on a genome with a _sensitive_ setting.
In the log file EDTA printed:
```
TE annotation using the EDTA library has finished! Check out:
Whole-genome…
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```
biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data atena
* checking for file ‘atena/DESCRIPTION’ ... OK
* preparing ‘atena’:
* checking DESCRIPTION meta-information ... O…
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RepeatModeler accepts a `-pa #` option to set the number of child processes it will fork, including for rmblastn tasks. However, [RepeatMasker::NCBIBlastSearchEngine by default invokes rmblast with `-…