User: genie66

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genie6620
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New User
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United States
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9 months, 2 weeks ago
Joined:
4 years, 7 months ago
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Posts by genie66

<prev • 18 results • page 1 of 2 • next >
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why and how multi allele gets reported during variant calling in vcf
... This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can only have two alleles(paternal and maternal) that way after variant calling, an allele at one posit ...
variant-calling vcf allele snp multi-allele written 9 months ago by genie6620
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Comment: C: Plot multiple bed files using R package Gviz
... Hi, thanks for you response. I couldn't do import.bed but `sample1 <- read.table("custom.bed",header = TRUE, sep="\t",stringsAsFactors=FALSE, quote="")` worked, but the DataTrack function shows the following error, `Error in .fillWithDefaults(range, defaults[missing], args[missing], len = nrow(r ...
written 12 months ago by genie6620
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Plot multiple bed files using R package Gviz
... Hi, I am new to R and looking for some help in plotting multiple bed files which may or may not overlap. They do have multiple chromosomes. I found a package called Gviz, where a Chromosome ideogram and genomic region could be plotted. But I am not sure how to load a bed file. I am aiming to plot p ...
R .bed gvi bed plot written 13 months ago by genie6620
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Zygosity of variants/allele in VCF
... I am new to bioinformatics and trying to understand the zygosity of variant/allele in VCF data. Couldn't find proper bioinformatics explanation anywhere, can someone please explain the difference between different zygosities(Hetero,homo, hemi) and these three in terms of compounded, inherited and do ...
gene allele zygosity variants written 17 months ago by genie6620
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Comment: C: Removing duplicate variants from the VCF file using Position,Reference base and
... No I dont want to sort them, that will disturb my further analysis. ...
written 3.0 years ago by genie6620
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Removing duplicate variants from the VCF file using Position,Reference base and Alternative base
... I have a merged VCF file of several samples and I want to remove duplicates from the master VCF based on the Postion,Reference and alternate base. Can Some one help me in out in either python or Linux commands. Thanks ...
vcf duplicate written 3.0 years ago by genie6620 • updated 3.0 years ago by 13en90
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Comment: C: How To Calculate The Rpkm For The Count Tables Of Rna Seq Data
... Is there any script available for calculating RPKM? I have a matrix ofGenes in the first column, gene_length in second column followed by count of all the samples in other colums. ...
written 3.1 years ago by genie6620
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Comment: C: VCF file REF column only contains N
... Thanks @jackfrost this following command worked for me. Hope it help someone samtools mpileup -uf hg19.fa SRR14819$i.sorted.bam | bcftools call -mv > SRR14819$i.Control.vcf ...
written 3.2 years ago by genie6620
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Comment: C: VCF file REF column only contains N
... When I add pipe, I am getting nothing after the header description. Do you find any mistake in the command? ...
written 3.2 years ago by genie6620
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VCF file REF column only contains N
... I am using samtools mpileup to call variant. Command used: samtools mpileup -u -f "/gpfs/home/g/o/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa" "/gopisiva/Mason/Single_cell/SC_Stressed/*.bam" | bcftools view -bvcg - > SC_Stressed.raw.bcf" bcftools view SC_Stressed.raw.bcf -v vcfutils.pl var ...
vcf ref samtools mpileup written 3.2 years ago by genie6620 • updated 3.2 years ago by jackfrost219970

Latest awards to genie66

Popular Question 11 months ago, created a question with more than 1,000 views. For VCF file REF column only contains N
Popular Question 13 months ago, created a question with more than 1,000 views. For Get Fasta -Protein Sequences for Given protein names(Homo sapiens)
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Get Fasta -Protein Sequences for Given protein names(Homo sapiens)
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Mapping peptide to the source genomic region
Scholar 4.6 years ago, created an answer that has been accepted. For A: Perl code to get starting and ending position of list of peptides from the prote

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