User: Evgeniia Golovina

Reputation:
940
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Trusted
Location:
New Zealand
Twitter:
@FoffaJn
Last seen:
1 week, 2 days ago
Joined:
3 years, 6 months ago
Email:
j**********@gmail.com

PhD student at the Liggins Institute, The University of Auckland.

Posts by Evgeniia Golovina

<prev • 53 results • page 1 of 6 • next >
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Comment: C: SAMtools mpileup and bcftools doesn't call InDels...
... The consensus-caller assumes only biallelic sites. Multiallelic caller - multiallelic sites. You can reads about the difference between biallelic and multiallelic sites here --> http://gatkforums.broadinstitute.org/gatk/discussion/6455/biallelic-vs-multiallelic-sites ...
written 18 months ago by Evgeniia Golovina940
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Comment: C: How bcftools isec works ?
... For intersecting more than two vcf files, you can use -n parameter (https://samtools.github.io/bcftools/bcftools.html#isec): bcftools isec -n=3 A.vcf.gz B.vcf.gz C.vcf.gz ...
written 2.1 years ago by Evgeniia Golovina940
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Comment: C: SNP call using bcftools
... Yes, technically, DV - is a number of high-quality variant reads that support each of the reported SNP. ...
written 2.3 years ago by Evgeniia Golovina940
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Comment: C: What is the difference between --split-files and --split-3 when using fastq-dump
... Split-files option outputs two fastq files in teh case of paired-end reads: one file - for forward, another - for reverse reads. ...
written 2.5 years ago by Evgeniia Golovina940
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Comment: C: What is the difference between --split-files and --split-3 when using fastq-dump
... is your data paired-end reads? or single-end? ...
written 2.5 years ago by Evgeniia Golovina940
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Comment: C: What is the difference between --split-files and --split-3 when using fastq-dump
... "--split-3 will output 1,2, or 3 files: 1 file means the data is not paired. 2 files means paired data with no low quality reads or reads shorter than 20bp. 3 files means paired data, but asymmetric quality or trimming. in the case of 3 file output, most people ignore .fastq . this is a very old fo ...
written 2.5 years ago by Evgeniia Golovina940
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Comment: C: What is the difference between --split-files and --split-3 when using fastq-dump
... Please, look there about split-3 option --> https://www.biostars.org/p/156909/ Also, please look there --> https://www.biostars.org/p/137228/#179501 - to see about --split-files option ...
written 2.5 years ago by Evgeniia Golovina940
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Comment: C: Where can I get exome vcf file from the 1000 genome project?
... I guess, no. I prefer to consider exome data as ones that obtained from Whole Exome Sequencing technology (WES) (library preparation includes enrichment for exon targets). Target exon regions (extracted from WGS data) may not be properly covered and if you plan to use them further in variant calling ...
written 2.6 years ago by Evgeniia Golovina940
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Answer: A: Where can I get exome vcf file from the 1000 genome project?
... Please, look there --> https://www.biostars.org/p/111262/ ...
written 2.6 years ago by Evgeniia Golovina940
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Answer: A: Bowtie2 sequence alignment of Baking yeast
... You can download whole Ensembl genome here --> ftp://ftp.ensemblgenomes.org/pub/fungi/release-29/fasta/saccharomyces_cerevisiae/dna/ Release 29, Assambly R64-1-1. In README file you can find more info about the dir content. This is unmasked (i.e. contains all repeats and low complexity regions) ...
written 2.6 years ago by Evgeniia Golovina940

Latest awards to Evgeniia Golovina

Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Ti Tv ratio and their usefulness in exome sequencing
Appreciated 11 months ago, created a post with more than 5 votes. For A: SAMtools mpileup and bcftools doesn't call InDels...
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: SAMtools mpileup and bcftools doesn't call InDels...
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: What's the difference between mpileup output and bcftools call ?
Appreciated 14 months ago, created a post with more than 5 votes. For A: What's the difference between mpileup output and bcftools call ?
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Teacher 20 months ago, created an answer with at least 3 up-votes. For A: SRA to BAM
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