User: Evgeniia Golovina

Reputation:
760
Status:
Trusted
Location:
Russia
Twitter:
@FoffaJn
Last seen:
1 month ago
Joined:
2 years, 6 months ago
Email:
j**********@gmail.com

I've been working for Genestack. Our aim is to build a really cool cloud-based Bioinformatics platform and help people to do bioinformatics faster not thinking about any formats. If you are interested in our platform, you can read more about Genestack features here.

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 6 months ago by Evgeniia Golovina760
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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 12 months ago by Evgeniia Golovina760
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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 14 months ago by Evgeniia Golovina760
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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 17 months ago by Evgeniia Golovina760
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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 17 months ago by Evgeniia Golovina760
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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 17 months ago by Evgeniia Golovina760
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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 17 months ago by Evgeniia Golovina760
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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 18 months ago by Evgeniia Golovina760
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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 18 months ago by Evgeniia Golovina760
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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 19 months ago by Evgeniia Golovina760

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Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: What's the difference between mpileup output and bcftools call ?
Appreciated 6 weeks 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 11 months ago, created an answer with at least 3 up-votes. For A: Ti Tv ratio and their usefulness in exome sequencing
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