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I am not sure to understand the meaning of this statement in the IBIS technical details.
>**3 Baseline Solutions**
>
>During the Leaderboard stage, the baseline for evaluating PWMs and AAAs …
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Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/656
### **Description**
**Sub-lineage of:** XBB.2.3.3
**Earliest sequence:** 2023-7-30, Netherlands, Noord-Brabant —…
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Hello, I'm running dNdS() on the cds of 2 species containing 13486 orthologous pairs, but only 1754 genes get the calculations done for. The rest runs into this error.
`ERROR: number of input seqs…
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I'm querying my .gff files to pull out sequences for certain genes but it is giving me output in amino acids. I saw in a supplementary document that you can get this outputted in nucleotides but the d…
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Currently, when we autodetect a new sequence file, we assume it is in the nucleotide alphabet, which is wrong. We need a function which, given a FASTA sequence file, does Deep Content Inspection to de…
leto updated
13 years ago
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Hello, thank you very much for providing the RTCR code. It helps with replacing mixcr for analysis.
However, I have noticed two issues:
I noticed that the nucleotide sequences for CDR3 in RTCR an…
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## Expected Behavior
Cluster nucleotide genome sequences (e.g., wgs records, contigs, scaffolds, complete genomes) in a few hours using `easy-linclust`
## Current Behavior
Running `easy-lincl…
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## Expected Behavior
Test and obtain the expected gene cluster.
## Current Behavior
### using CDS
When I use the gff file generated by prokka, it prompts "Not enough columns in GFF file" `./space…
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
The issue existed in both bulk and single-cell mode
**Describe the bug**
When using Salmon to quantify non-red…
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Hi. I tried to use easyfig.py from the command line. It worked fine for tblastx, but it seems not to be working for blastn. Apparently, makeblastdb is not been triggered when the option is blastn. Cou…