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Hi,
When I try to run quickmerge using assembly A as reference (Illumina assembly ~746MB) and assembly B (nanopore assembly ~846MB) as query, it works fine.
However, when I switch assembly A as…
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I have found that many protein sequences of the fasta file do not appear in the id2genemap.txt file. I have been working with the latest release available ([PCycDB v1.1](https://github.com/ZengJiaxion…
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Hi,
When I running this command :
`vcf2maf=/data/jiaf/wes_cancer/biosoft/vcf2maf/vcf2maf.pl
vep_path=~/miniconda3/envs/vep/bin/
GENOME=/data/jiaf/wes_cancer/biosoft/gsutil/gatk/hg19/v0/Homo_sapie…
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Many libraries support streaming FASTA/FASTQ data through stdin. It would be pleasant for that mode of operation to be supported as it is handy when writing small stream processors
```bash
$ cat t…
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List of needed features and modifications
- [x] Personal database implementation
https://github.com/ImagoXV/NanoASV/commit/a48298e33ebc8c7b62db2f117e6a6d5e207543f7 - Personal database OK. Ind…
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CONTEXT
When invoked without optional arguments, only the necessary "--input" bb_get_fasta info displays all data in tabular format, like this:
Seq_id header sequence
If the script is invoke…
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I guess it is maybe not needed as it can be done by hand, and it is definitely nothing fancy, but think it would be really nice if also PeptideShaker could do it. so something like Mascot does:
![ima…
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**1. What were you trying to do?**
- Produce a VCF from a mapped GAM
```
vg call graph.gbz --pack graph.pack --snarls graph.snarls --genotype-snarls --all-snarls --gbz-translation --gbz > ex…
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**Describe the issue**
I am executing this command as per 'box 2' in Nat. Biot. 2024 article:
~$ kb ref -i fpa_index.idx -g fpa_t2g.txt -f1 fpa_cdna.fasta cds_from_genomic.fasta genomic.gtf
**W…
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Greetings. I keep getting an error message 'Protein doesn't have the full sequence' when using spectral count. My PSM file data input (named 'score') is in the format of Crux tab delimited, but the da…