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Recent Replies
Answer: Filtering based on alternate allelic balance
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Arton
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I found the answer when using bcftools. Is there is a way to do this with FilterVcf?
bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
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Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf
> 1:2114:12111:13792
That is part of …
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Mathew
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Hi, here is a breakdown of each part that you asked about:
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I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
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I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
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Should be possible: https://www.biostars.org/p/430366/
Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
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Fungal genetics
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Hi,
Below SNPEff database building error I am getting.
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The headers are correct and sam…
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the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
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You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
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Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
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Two last seats have just become available. Apply now, if you want them.
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You always need to add the following option when you are using `-p` to count paired-end reads.
--countReadPairs If specified, fragm…
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