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Similar to how we write a spikein report, we should consider adding a report on insert sizes via Picard's `CollectInsertSizeMetrics`.
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Thank you all for developing CoRAL. I have a question regarding the error message during infer_breakpoint_graph step and wonder if there are any suggestions you could kindly have:
Error message:
T…
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Would it be easy to make --minimum-mapping-quality to haplotypecaller a parameter in the pipeline?
One thing that we (@marcelm and I) are interested in is to better set the MAPQ score in strobealig…
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Hello,
Is there are reason why the read name information needs to be concatenated here?
https://github.com/ulelab/ultraplex/blob/be1841f65bdd14d310dadc4a4927028593d5cd1e/ultraplex/__main__.py#L5…
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Hello I am trying to run the PASA training step (v. 1.8.11) with the following command but I get the following error
funannotate train -i $genome --cpus 1 -o $outdir -l $left -r $right --trinity $t…
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Is it possible to allow any nucleotide to map to a specific location without penalty?
For example, we have a reference sequence: G*AC, where * can be any nucleotide.
We want to allow GAAC, GTAC, G…
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```
/usr/lib/python3.5/site-packages/quast-4.5-py3.5.egg/EGG-INFO/scripts/quast.py assembly_metrics/sample_data/BCM-After-Atlas/Contigs/Clec_Bbug02212013.contigs.fa.gz
Version: 4.5
System infor…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.8
- OS name and version (`lsb_release -ds`): Ubuntu 20.04.3 LTS
**To Reproduce**
Exact bcbio command you have used:
```
bcb…
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## Current behaviour
Section 2 (recommended practices) of the SAM spec states "_For a unmapped paired-end or mate-pair read whose mate is mapped, the unmapped read should have RNAME and POS identical…
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Is strobealign a good basis for the following application:
We would align against a pangenome FASTA. So we might have 100 genomes in this system. Downstream we project the alignments into a graph f…
ekg updated
11 months ago