User: Evgeniia Golovina

Reputation:
820
Status:
Trusted
Location:
Russia
Twitter:
@FoffaJn
Last seen:
2 days, 5 hours ago
Joined:
2 years, 8 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 7 months ago by Evgeniia Golovina820
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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 14 months ago by Evgeniia Golovina820
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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 16 months ago by Evgeniia Golovina820
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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 19 months ago by Evgeniia Golovina820
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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 19 months ago by Evgeniia Golovina820
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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 19 months ago by Evgeniia Golovina820
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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 19 months ago by Evgeniia Golovina820
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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 20 months ago by Evgeniia Golovina820
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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 20 months ago by Evgeniia Golovina820
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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 20 months ago by Evgeniia Golovina820

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Appreciated 27 days ago, created a post with more than 5 votes. For A: SAMtools mpileup and bcftools doesn't call InDels...
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: SAMtools mpileup and bcftools doesn't call InDels...
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: What's the difference between mpileup output and bcftools call ?
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