Comments (2)
ar0ch
commented on August 26, 2024
Hi Alejandra,
STing (really the seqan library we're using) doesn't support the extended DNA alphabet (BDHKMRSTVYW). So you'll need to replace those characters with Ns. This sed command should work for most fasta files: sed -e '/^[^>]/s/[^ATGCatgc]/N/g'
We didn't see a significant impact on ST call accuracy with these edits.
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AleSR13
commented on August 26, 2024
That's what I assumed but didn't know what to replace it for. Thank you very much, it worked now! Hope the next part works too.
from sting.
Related Issues (15)
- Rewrite git history for publication
- Could not open the input file 'ERR026529_1.fastq.gz' HOT 3
- cgMLST schemes? HOT 21
- finding rST through rMLST scheme HOT 2
- Profile file for cgMLST HOT 3
- indexer reports "ERROR: The config file does not contain the [loci] section." HOT 1
- Preparing the database missing from README
- Is it possible to use assembly instead of NGS raw reads?
- Check licensing info HOT 1
- Automated STing MLST db
- subprocess.CalledProcessError HOT 5
- Proper usage of index HOT 4
- db_util.py not able to download data from PubMLST HOT 1
- Missing files HOT 2
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