User: ernestrv0101

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Posts by ernestrv0101

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Comment: C: Basics about sequencing/alignment and variant calling
... Thanks for the clarification, d-cameron. So when you said: > is generally only ever done when creating a reference genome for that organism. you mean when creating a reference assembly like: https://www.biostars.org/p/75489/ So in that case, it just takes the most common variations for each p ...
written 3 months ago by ernestrv01010
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Basics about sequencing/alignment and variant calling
... I am new on bioinformatics, and I am not biologist. I have a basic questions about sequencing/alignment and variant calling. For example in humans, I understand that the DNA mutates all time, so during the process of sequencing, for one specific locus, in theory we only expect two variations (diploi ...
variant calling alignment sequencing written 3 months ago by ernestrv01010 • updated 3 months ago by d-cameron1.8k
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Comment: C: Alignment & Variant Calling explanation SNP and SNV.
... @finswimmer OK so leaving aside the definition of SNP or SNV, they just extract the variations against a reference (identifying and discarding the possible errors, misalignments, etc). I was confused with the SNP's definition. Thanks! It is an insect but thanks anyway @Titus! ...
written 3 months ago by ernestrv01010
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Alignment & Variant Calling explanation SNP and SNV.
... As a beginner, I have a basic question about a bam alignment. After map my fastq reads (from a single individual) to a reference (bwa), I can see the variations, which I guess it includes sequencing errors, misalignment, errors in library preparation and real SNPs. In an haploid organism, I suppose ...
vcf ngs alignment map to reference written 3 months ago by ernestrv01010 • updated 3 months ago by Biostar ♦♦ 20

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