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Does babette work with amino acid sequence alignments?
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Dear Edgardo, Ive noticed that when adding reference sequences to alignments, prior to informed paralog filtering, in some cases these are added in the reverse direction to the extracted sequences in …
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I have double, triple, quadruple checked that my input files are all in the correct format but I consistently get this error message which halts the run. Alignment seems to work perfectly and I have o…
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Hi,
I wonder if anyone in this community can help me figure out the reason behind the discrepancy in counts. Please see below:
I am using HTSeq-count to generate counts from two different types …
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Hi,
I am trying to assemble the genome of a worm, and I was hoping that minipolish would detect the mitochondrial genome and output it in the gfa file.
I have sequencing one of my worm species a l…
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These genes have had revised structures which means that they
These genes do not have signal peptides because the sequence does not match the UniProt sequence at the N-term.
https://www.pombas…
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[Class `ProteinEmbedding`](https://github.com/scikit-bio/scikit-bio/blob/545c9859635a5b8514bd9fd599475717c533f108/skbio/embedding/_protein.py#L29-L121) implements a data structure for the storage of p…
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Hello, I need the sequence from part of my Blastp hits. The full_sseq option from custom outfmt 6 returns the sequence with variable amino acids.
For example:
MIRSRSRATRGVRMKTFKATMTTAMLALXXXXXXXXXX…
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Hi again,
I have another question, is there a way to retain the reads that map to each reference taxon? I have looked at the various options for output-type and do not see the option to output the …
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Since the sequence-error.tsv file has the errors for all of the alignments, knowing the map_name is helpful to filter this file.