Moderator: finswimmer
finswimmer ♦ 14k
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Posts by finswimmer
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C: how to unique a file row-wise?
... Hello https://www.biostars.org/u/21479/,
how is this question related to bioinformatics? Is the order of the numbers per row in the output important? If so, how is the relationship to the input?
fin swimmer ...
written 8 days ago by
finswimmer ♦ 14k
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... Hello https://www.biostars.org/u/25073/,
> But I can't use bcftools consensus because it will not generate a consensus sequence from a FASTA reference containing multiple sequences.
can you add more information what you mean by this and how it looks like? A fasta file can contain multiple seq ...
written 8 days ago by
finswimmer ♦ 14k
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... Interesting, I don't know why `bcftools` is missing that much variants here. I was able to reproduce it.
In my experience [freebayes](https://github.com/freebayes/freebayes) is the better choice if you are mainly interested in indels. In a short test it finds variants in 400 positions. ...
written 27 days ago by
finswimmer ♦ 14k
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... The second sequence is the reverse complement sequence of the first one. So the variant 227G>A is 309 C>T in the second. And 245C>G is 290 G>C in the second. Looks all good to me. ...
written 4 weeks ago by
finswimmer ♦ 14k
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... Hello https://www.biostars.org/u/79298/,
you should show us, how your data looks like exactly. Otherwise we can just guess.
fin swimmer ...
written 5 weeks ago by
finswimmer ♦ 14k
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... Hello,
AFAIK `freebayes` assumes by default, that your sample is diploid. So it will never give you more than two alleles for a specific position.
Of course there are some parameter you can use, to get more information. `freebayes --help` is mentioning a combination of parameters that looks promis ...
written 5 weeks ago by
finswimmer ♦ 14k
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... The choice of the distribution isn't that important. Choose any more or less current one. To install and manage your bioinformatics tools use [conda](https://docs.conda.io/en/latest/miniconda.html) with the [bioconda channel](https://bioconda.github.io/user/install.html) activated. The first part of ...
written 5 weeks ago by
finswimmer ♦ 14k
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... Hello https://www.biostars.org/u/49704/,
why do you want do convert to a reference genome that is outdated for 7 years now?
fin swimmer ...
written 12 weeks ago by
finswimmer ♦ 14k
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Comment:
C: FASTA file header
... > However, after aligning to reference, vcf ID from the header disappears,
Can you show an example of your expected output? ...
written 12 weeks ago by
finswimmer ♦ 14k
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... Hello,
according to [this docs](https://gslweb.discoveryls.com/information/software/bam2fastq) `bam2fastq` assumes that each read is aligned only once in the bam file. This is rarely the case. There are always a bunch of reads that are mapped multiple times. So I guess `bam2fastq` will extract the ...
written 12 weeks ago by
finswimmer ♦ 14k
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