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I aligned 38 sequences, average length 72, but including one outlier sequence with a length of 505 and C-terminal homology.
Same thing happens with muscle or belvu. Alignment is long , but I expe…
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Hi Yan,
I use abPOA to generate a consensus from four sequences. Here is the distribtuion of n_seq / n_cov in each base in the consensus sequence. My question is, is there a way to remove low cover…
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Dear tandem-genotypes developers,
I am using tandem-genoypes v1.8.3 to obtain consensus sequences for the two alleles.
After running the alignment with last, I am running:
```
tandem-genotypes -…
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Hi,
I would like to request more features for `pxconsq` function in **phyx** :
1. have a flag (or option) that user can choose preferred symbol for gap? Like "-" or "N", or no gap generated …
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I noticed this consensus sequence:
```
@6 10A0C2T4G0 11A0C4T2G0 15A0C2T4G0 16A0C4T2G0 17A0C2T4G0 18A0C4T2G0 24A0C2T4G0 45A4C0T2G0 46A4C0T0G2 48A1C0T0G5 49A0C4T2G0 56A2C4T0G0 58A5C0T1G0 64A0C1T0G5 66A…
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I have many similar sequences of different lengths and need to get the consensus of them.
From the docs, the seq module should work for this, but any example provided?
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Following the discussion in PR https://github.com/bulwark-security/bulwark-community-ruleset/pull/1, there's a consensus on improving the function to gracefully handle invalid UTF-8 sequences. The '�…
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I ran similar commands with the same data, only changing the -H setting.
`bcf consensus -H 1 -f reference.fa subject.vcf.gz > consensus_H1.fasta`
`bcf consensus -H 2 -f reference.fa subject.vcf.gz…
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Hello,
I'll be soon getting data RNA-seq data with UMIs, and I was interested in running pair consensus decoding on the data. I noticed the paper's and bonito's implementation takes the reverse com…
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What are we expecting to see in this data. eg Are there barcodes?
It appears to be a 1 GB fasta file (which is a bit odd as fasta does not have quality info) filename: `R2C2_Consensus.fasta`
seq…
sr320 updated
2 months ago