Moderator: finswimmer

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finswimmer12k
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Posts by finswimmer

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Clipping primer after alignment
... 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 ...
clipping bam written 14 hours ago by finswimmer12k
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Comment: C: How to generate consensus fasta uninterleaved from bam?
... 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 finswimmer12k
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Comment: C: Generation of incorrect heterozygous calls after left normalization using bcftoo
... 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 finswimmer12k
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Comment: C: Generating consensus sequence from bam file
... 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 finswimmer12k
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Comment: C: Generation of incorrect heterozygous calls after left normalization using bcftoo
... Hello, please provide an example dataset one can use directly for testing. Thanks! fin swimmer ...
written 2 days ago by finswimmer12k
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Comment: C: bcftools merge creates high missingness rate
... 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 finswimmer12k
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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 finswimmer12k
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Comment: C: Consensus sequence from multiple BAM files on a single position
... 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 finswimmer12k
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Comment: C: bedtool getfasta only reads the first line of my bedfile
... 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 finswimmer12k
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Answer: A: 1000 Human Genomes Project Population Alignment Data
... Hello, the corresponding alignment files are here: * https://www.ebi.ac.uk/ena/data/view/PRJEB31736 fin swimmer ...
written 7 days ago by finswimmer12k

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Teacher 22 hours ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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Popular Question 23 days ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Which human reference genome should I use?
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