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I have been using GOA tools the latest zipped version, and getting the below error that only few input genes are in the background population. Is there a way to get through this error or is it that it…
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I'm having difficulties understanding and tuning the confidence threshold. According to the documentation here, the confidence score is C/Q, where C is the number of k-mers supporting a particular tax…
fm361 updated
2 years ago
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Hello,
I have been trying to follow the steps to generate a kraken2 db of all bacteria. I've run the commands
`kraken2-build --threads 8 --download-taxonomy --db all_bac`
`kraken2-build --down…
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I have Kraken2 installed with conda and I am trying to build a database. I have done this before with no problems but today I am getting errors - it seems others are too.
```
`rsync_from_ncbi.pl: …
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I will appreciate if you can help me with a couple of questions regarding
MMseqs2. I've been running it using both approaches, for the alignment against
sequence dbs (mmseq search -> convertalis) an…
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Hi,
I'm trying out using `kraken2` for the first time. I have short (150 bp) sequencing reads that are ostensibly of SARS-CoV-2, but as part of QC I wish to classify them using `kraken2` to see if …
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Hello, thank you for your help in advance.
When running the db_installer.sh command I get the following message come up:
gi_taxid_prot.dmp.gz dowloaded
db_installer.sh: 88: db_installer.sh: [[: not …
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Running `python3 ui/egapx.py ./examples/input_D_farinae_small_rnaseq.yaml -e docker -o example_out` gives me the following result:
```
!!WARNING!!
This is an alpha release with limited features a…
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Dear developer,
I'm using the GTDB database to assign the taxonomic label for my contigs, I have downloaded the GTDB from the predefined database by the command `mmseqs databases GTDB /my_path/GTDB …
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https://ftp.ncbi.nih.gov/genomes/
https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/
List of `refSeq` sequences: https://ftp.ncbi.nih.gov/genomes/refseq/assembly_summary_refseq.txt
Example: [direc…