29 results in 0.0030 seconds.
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Problem getting reference genome WBcel235
I am unable to get Caenorhabditis elegans reference genome in fastqsanger format from any option of 'Get data'. My FTP server is not functioning. How... -
mapping multiple low cov genomes to one ref genome
We are starting a project to explore admixture between populations of two species. We have over 40 low coverage genomes (1-5x coverage) (lcg) and a very... -
Genome Assembly vs Reference Genome for slicing around mutation location
Hello friends,
I have a bam file and corresponding vcf file from some source. I am trying to slice the DNA across its mutation... -
GIAB NA12878 dataset
Hi all,
first of all must say I'm a newbie in NGS and a completely inept in forums like this, so dont blame me too much. In fact its my first...Last edited by NielQC; 11-09-2016, 10:48 AM. -
remove scaffold and other unplaced sequence before mapping?
Hi,
I downloaded reference genomes from Ensembl (fasta format). But there are lots of sequences with name "dna:scaffold": https://git...Last edited by yong peng; 03-27-2016, 07:30 PM. -
Convert .fna file from NCBI to .fa or .fasta file
Hello,
I am totally new to this (I am a student following a course in bio-informatics) and I wanted to use a genome found on NCBI (in .fna or genbank... -
SNP flanking regions with "pseduo"-reference & viewing all alignments around SNPs
Hi everyone,
Sorry for the long post but I could really use your help! I'm trying to verify flanking regions around SNPs and worried about... -
A better way to map sequencing reads using existing read mapping tool
Our group just published a paper on improving sequencing read mapping. We achieved this without inventing a new read alignment tool. The key is to customize... -
Do variant callers miss rare variants in reference? [Super Explanatory Image Inside]
Generally variant calling programs (such as GATK-UnifiedGenotyper) look for differences between reference genome and submitted sequence. However, we all... -
Merging different reference genomes
Hi to everyone,
i'm trying to replicate a pipeline from an article in which they says that they had merged different information from different... -
How to generate random short reads from a reference genome
Hi,
I am in the process of generating accuracy benchmarks against different assembly algorithms/tools (including one of my own). Is there... -
iGenomes reference genome not accurate?
I grabbed the mm9 reference genome from iGenome. When running cuffcompare, I noticed that the genes.gtf refers to chr#_random whereas the chromosome folder... -
Blast to reference genome
Hello!
I have a bit of a conundrum with Blast of all things. I have it locally installed on a Mac. I have individual fasta files of sequences... -
get sequence context from a reference genome
hi, everyone.
If I have a tsv file of somatic mutation profile that contains information of:
1. mutation information (for example, a mutation... -
how much of the MHC is represented in the reference genome?
I remember that former versions of the reference genome (at least hg18) used to lack some genes due to compression of the sequences to one prototype in...
