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How does VSEARCH scores alignments on masked regions? I would expect it to discard hits between masked regions but, when clustering the sequences:
```
>HWI-ST397:349:C2YYMACXX:3:1102:20033:76341…
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Hi, I ran this command to perform Isoquant quantification with the aim of obtaining transcript quantification results for all samples: isoquant.py --reference genome.fa --genedb ./merge.combined.gtf -…
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The command
cat metadata.txt | grep Dec | grep complete | grep -v gapped | cut -f 1 > early.ids
returns no lines from the metadata.txt file
I believe it's because the dates are in numeric for…
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Dear@mijiandui
Reference checkV tutorial:
Finally, perform UCLUST-like clustering using the MIUVIG recommended-parameters (95% ANI + 85% AF):
aniclust.py --fna --ani --out --min_ani 95 --min_tc…
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**Hello igraph community!**
I would like to see an extension of the configuration model implemented, that allows one to specify the joint degree/triangle sequence of a graph. See reference below...…
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I.e. in when clustering TCRs on amino-acid similarity it might be nice to return a string that encapsulates the conserved sequence, with a wild-card character (maybe %D:N, for example suggesting that …
n-hal updated
2 months ago
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Hi, Thanks always for the nice tool!
I have clustered a large sequence set with `mmseqs linclust `, and now I want to add some sequences and update the clustering result with `mmseqs clusterupdate`.
…
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When trying to figure out how to document metabarcoding data, I came across some things that were not super clear to me.
Any insight in this question is much appreciated, and perhaps the terms could …
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## Expected Behavior
searching against MMseqs2 databases after clustering step
## Current Behavior
after mmseq2 db creation (giving a type nucleotide db) and clustering, it does not proceed due t…
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Hello,
I am running lotus2 only for taxonomy assignment of ITS1 sequences (so -taxOnly) (which is great! works super fast). I assumed that the output file would contain the same number of sequences…