User: anastazie.d

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anastazie.d30
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New User
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Czech Republic/Prague/HPST
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AnastassiyaZidk
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1 year, 10 months ago
Joined:
4 years, 8 months ago
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a**********@gmail.com

about me

Posts by anastazie.d

<prev • 10 results • page 1 of 1 • next >
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Answer: A: How to Find OMIM id's of Disease Corresponding to a List of Gene Symbols in R?
... Hi, I had similar problem. I had list of gene names and ENSEMBL IDs and I wanted to get OMIM IDs. I used R package [org.Hs.eg.db][1] and following code, where `overlapDf$gene` are gene names. ``` library(org.Hs.eg.db) ``` ``` cols <- c("SYMBOL", "GENENAME", "ENSEMBL", "OMIM" ) ``` ``` mappedGe ...
written 2.4 years ago by anastazie.d30
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Comment: C: Calculating Gc Content For All Ccds
... `fastaFrombed` is not working anymore. Use `bedtools getfasta` ``` Tool: bedtools getfasta (aka fastaFromBed) Version: v2.24.0 Summary: Extract DNA sequences into a fasta file based on feature coordinates. Usage: bedtools getfasta [OPTIONS] -fi -bed -fo Options: -fi Input FASTA file - ...
written 2.4 years ago by anastazie.d30
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Answer: A: Illumina basemount copy files error
... Hi, Finally I solved this problem with brute force approach. I checked if the files were truncated by: gunzip --test file.fastq.gz Then I downloaded truncated files manually. ...
written 2.8 years ago by anastazie.d30 • updated 12 weeks ago by RamRS19k
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Comment: C: Illumina basemount copy files error
... ls -la "/home/nasta/Public/BaseSpace/Projects/Haloplex/Samples/Hi5-1/Files/Data/Intensities/BaseCalls/Hi5-1_S2_L001_R2_001.fastq.gz" -r--r--r-- 1 nasta nasta 98851092 Sep 26 07:45 /home/nasta/Public/BaseSpace/Projects/Haloplex/Samples/Hi5-1/Files/Data/Intensities/BaseCalls/Hi5-1_S2_L001 ...
written 2.8 years ago by anastazie.d30 • updated 12 weeks ago by RamRS19k
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Illumina basemount copy files error
... Hello everyone! I started to use [basemount][1], which is command line tool to access data on BaseSpace. I first mount filesystem and then use cp command to copy file to my computer. Copy of some files is OK, but for approximately 1/3 files I get following error: cp: error reading '/home/nas ...
genome illumina next-gen written 2.8 years ago by anastazie.d30 • updated 11 weeks ago by RamRS19k
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Merge BEAGLE .gprobs files
... Hi, I have two files in BEAGLE .gprobs format containing genotype probabilities for SNPs that I want to merge. Is there any software that can do that? Input files: 1. output from ANGSD software, crated using following command: ./angsd -GL 2 -doGlf 2 -bam /media/4TB2/Ngsadmix/bamlist.txt -doMajo ...
snp beagle written 4.0 years ago by anastazie.d30
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Answer: A: SNP varian calling - decreased number of SNPS with increased coverage?
... Hi everyone, finally it was problem with folders removing during re-running bcbio-nextgen. I had opened this issue here https://github.com/chapmanb/bcbio-nextgen/issues/593   Thanks for comments, Anastassiya ...
written 4.2 years ago by anastazie.d30
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Comment: C: SNP varian calling - decreased number of SNPS with increased coverage?
... It was genome sequencing. Here are values for both analyses for two samples: Cleaned Sample 1 Mapped reads:      890944806 Mean coverage:     29.6981602 Sample 2 Mapped reads:      659515763 Mean coverage:     21.983858767 All Sample 1 Mapped reads:      1829469743 Mean coverage:     60.982324767 ...
written 4.2 years ago by anastazie.d30
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SNP varian calling - decreased number of SNPS with increased coverage?
... Hi all, I am working with Illumina Hiseq 2000 DNA-Seq data from 2 human saliva samples. Two runs were performed per each sample: cleaned (human DNA cleaned from bacterial DNA) and non-cleaned. My aim is to extract SNPs with rsID. To process fastq.gz files I used bcbio-nextgen package (https://bc ...
dna-seq vcftools bcbio-nextgen snp coverage written 4.2 years ago by anastazie.d30
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Software package for iCLIP data analysis
... Hi, I am newbie in RNA-Seq analysis and I need to analyze iCLIP data. Do you have any ideas about suitable R package or any other tools for statistical analysis of iCLIP data (normalization of iCLIP data particularly)?   Thanks ...
R rna-seq written 4.6 years ago by anastazie.d30 • updated 4.6 years ago by Jason870

Latest awards to anastazie.d

Popular Question 22 months ago, created a question with more than 1,000 views. For Software package for iCLIP data analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Software package for iCLIP data analysis
Scholar 2.8 years ago, created an answer that has been accepted. For A: Illumina basemount copy files error

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