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It would be very useful to report the total number of reads alinged to viral genomes and the fraction of reads aligned to each viral genome with respect to the total number of reads in a sample.
The…
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Perhaps what I am about to describe goes against the accepted method for adding to a new kraken2 database.
Here are the steps that produced the error:
Masking low-complexity regions of new file.…
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Dear, developers! I have the following problem.I used assembled contigs for virMine,command line was
```nohup python2.7 /virMine.py -A /MyData/Megahit_cross_assemble/final.contigs_over10k.fa -t 40 -…
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Hello,
I was wondering how exactly VirSorter defines a prophage regions and if there is a way to get the coordinates of the prophage regions identified?
Thanks,
Niamh
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In omicron SC2 sequences there is difficult area (3 bp deletion - 8 bp - 9 bp insertion). Typical aligners produce more soft clips than insertions.
![image](https://user-images.githubusercontent.c…
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Hello,
thanks for AA! It works class!
I was wondering if I can use my own fasta file (used to generate the bam)?
Maybe you can give a brief explanation about the data_repo folder structure. Should…
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From the Handbook:
https://www.ncbi.nlm.nih.gov/books/NBK53714/#gbankquickstart.i_have_viral_sequence_da
- [ ] CDS feature(s) with product name(s), nucleotide locations, and amino acid translation…
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I need to count the reads mapped to my viruses found via VirSorter2. However, I've already mapped to the contigs and I would like to use featureCounts to pull out the reads mapped to the viruses (not…
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Dear Simon,
I've been running VirSorter on the cyverse platform before, and now installed it on a server (CentOS Linux 7), as I'd like to use it for a larger number of samples. I followed the insta…