41 results in 0.0031 seconds.
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Bcftools installed via Cygwin plugin error
Hi! I am trying to look at several genomes of different individuals of the same species and call the SNPs for each genome using bcftools. I installed... -
Visualize just non-synonymous variants in IGV
Hello,
I used snpeff to annotate a set of variants and I would like to only visualize where a particular type of variant (non-synonymous... -
vcftools flags --mac and --max-mac give empty output
Hi everyone!
I'm a newbie in NGS data analysis, that’s why I’m asking for some help in things that might be easy in fact.
I have... -
VCFtools whole genome data zipped
Hi all!
New here, introduction: I investigate inbreeding in an endangered species where I have whole genome data of several individuals and variants... -
Finding SNPs that have been pre-defined
Hi All,
This is a bit of a beginners question but here goes....
I have a dataset of Illumina paired-end reads mapped to... -
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Bioinformatics for Cancer Ge... -
Nucleotide variation from multi-sample vcf file
Dear all,
I have an SNP information's from single vcf file consists of muti-samples (44 individuals). In order to get the nucleotide variations... -
Brainstorming "ddRAD-BiS"
Hi there,
I'm a newbie with sequencing, and I'm currently thinking about new ideas for a grant application. I work on non-model organisms... -
Transforming .ped files back to .vcf with original chrom. name
I am currently working on trying to obtain the general statistics on a set of SNPs. I have the original vcf file that I used in Plink to analyze for LD,... -
Calculating coverage of SNPs
Hello all,
I'm having a problem calculating the depth of coverage of a set of known variants (SNPs). What I want to know is 1) what percentage...Last edited by aprilw; 08-28-2015, 04:31 AM. -
Counting the total number of SNPs in a transcript
Hi,
I have RNAseq data that has been aligned to reference transcriptome and the aligned bam file is sorted and indexed.
... -
Bcftools stats
Hi everyone,
I'm studying how to use bcftools and playing a little bit with its parameters to better understand what they really do. I... -
Effects of Heterozygous and homozygous SNPS on RNA and Protein expression
Hello everyone, my name is Mamjoy. I am very new to this site but have been following the site keenly.
I have a question and I will be glad if... -
Simulating a genome with known SNPs
Does anyone know of a way to generate a simulated bacterial genome with known SNPs and indels relative to a given reference? I'd like to be able to generate... -
Data format - Unusable to R and Plink
Hullo! Apologies for the seemingly basic question but I am in knots over this and hope there is some help.
I have recently 'inherited'...
