Moderator: finswimmer
finswimmer ♦ 12k
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Posts by finswimmer
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... Hello everyone,
we are doing targeted sequencing using a Qiagen Kit. During library prep the dna is fragmented and tagged with umi and a universal primer sequence at one end of the strand. So for the enrichment only one specific primer per amplicon is needed.
I would like to clip the primer sequen ...
written 14 hours ago by
finswimmer ♦ 12k
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... Hello https://www.biostars.org/u/58200/ ,
you seems to be puzzled by what information all the different filetypes contain. I guess your question here is related to the one in you [other thread][1]? Have you take a look at the [tutorial][2] I've linked to [over there][3]? Is this what you are lookin ...
written 1 day ago by
finswimmer ♦ 12k
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... Hello,
that's better then nothing. But the input vcf would be more useful. Reduce it to some example lines that show your problem. ...
written 2 days ago by
finswimmer ♦ 12k
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... According to the [manual](http://www.htslib.org/doc/bcftools.html#consensus)o this should be possible with the `-I` argument:
-I, --iupac-codes
output variants in the form of IUPAC ambiguity codes ...
written 2 days ago by
finswimmer ♦ 12k
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... Hello,
please provide an example dataset one can use directly for testing.
Thanks!
fin swimmer ...
written 2 days ago by
finswimmer ♦ 12k
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... Hello,
> meaning all copies of the second allele have been replaced with missing genotypes
could you please provide an example of what you mean by this?
Is `bcftools merge` the right command for you? This is used to combine multiple vcf files from different sample(names). Why do you use the `- ...
written 3 days ago by
finswimmer ♦ 12k
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Comment:
C: multi sample vcf to data matrix
... Hello https://www.biostars.org/u/10432/ ,
could you please provide an example of your input and how your output should look like bases on this example?
fin swimmer ...
written 3 days ago by
finswimmer ♦ 12k
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... Hello,
to get the consensus sequence you first have to call variants (mpileup isn't enough) and then create the the consensus sequence with the help of your vcf file and the reference sequence. See here: https://www.biostars.org/p/367960/
fin swimmer ...
written 3 days ago by
finswimmer ♦ 12k
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... Could you please upload an extract of your bed file that doesn't work to somewhere, so we can take a closer look on that?
Also please show the exact bedtoools command you were using.
Thanks. ...
written 6 days ago by
finswimmer ♦ 12k
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... Hello,
the corresponding alignment files are here:
* https://www.ebi.ac.uk/ena/data/view/PRJEB31736
fin swimmer ...
written 7 days ago by
finswimmer ♦ 12k
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