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Questions tagged [genome]

Genome is the entirety of an organism's DNA sequence. The genome includes both the genes and the non-coding sequences, such as repeats, introns and regulatory sequences, possessing both known and unknown function.

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Map SNP IDs to genome coordinates

I have several SNP IDs (i.e., rs16828074, rs17232800, etc...), I want to their coordinates in a Hg19 genome from UCSC genome website. I would prefer using R to accomplish this goal. How to do that?
user1938809
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where do i download gene expression data?

i wanted to download gene expression data derived from generated by microarray experiments. i do not know too much about this subject, but as i understand, rows often correspond to genes and columns corresponds to samples. ideally, i expect a matrix…
Jane Wayne
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Can I use the Music Genome Project?

Is there an API or database I can access or is it a proprietary project?
HahaHortness
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NEAT: Speciating

I was trying to implement neat myself, using the original paper but got stuck. Let's say that in the last generation I had the following species: Specie 1: members: 100 avg_score: 100 Specie 2: members: 150 avg_score: 120 Specie 3: …
Finn Eggers
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What's a sensible way to represent a binary genome for a genetic algorithm?

My previous question belied my inexperience and was based on an assumption. Now I am much wiser. (Put 1s and 0s in a string? Pah! I laugh at the suggestion!) My question is then, how should I encode my genomes? On paper, they look like…
Tom Wright
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Subtracting two GRanges objects from each other

I've looked around and it doesn't seem like there were any questions posted before regarding this. I have two GRanges object with some coordinates, and I would like to subtract the intervals of one from the other. This is different from finding…
user3245575
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Extracting certain locus from multiple samples from text file

After profiling STR locus in a population, the output gave me 122 files each of which contains about unique 800,000 locus. There are 2 examples of my files: SAMPLE CHROM POS Allele_1 Allele_2 LENGTH HG02035 chr1 230769616 (tcta)14 (tcta)16…
Bách Nguyễn
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TypeError: on heapq.heapop on python3 but but working in python2

I am working on a genome compression algorithm using variations of Huffman coding. I have the following piece of code in python2: def makeHuffTree(trees): heapq.heapify(trees) while len(trees) > 1: childR, childL = heapq.heappop(trees),…
Manoj Agrahari
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"Killed" message while using Velvet to assemble SRA reads

I'm having some trouble using Velveth to assemble reads downloaded from the NCBI SRA. The command I used was: velveth velvet 27 -fastq -shortPaired -interleaved /home/bilalm/H_glaber_quality_filtering/AfterQC/good_reads/SRR530529.good.fq (velvet -…
Billy
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How to get elements from javascript file and put them into HTML elements

So I'm very new to HTML and I was trying to take an txt output file, convert it into usable data, and input that data into HTML, changing various attribute values, like title and innerHTML As an example, I was trying to use…
Lauren Kenyon
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No reads mapped in proper pairs, in paired-end sequencing bamfile using samtools

I am working with a bamfile of paired-end whole genome sequencing, and want to filter out reads from a specific genomic region that are not mapped in a proper pair (these sometimes indicate a structural variant). I am using samtools, and tried to…
Lisa
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Error in breseq during running bowtie2

I recently tried to use breseq to analyze a few bacterial sequencing data. However, I got a fatal error when breseq used bowtie2 to align the raw data to the reference genome. Here is the critical part of the error that I got: +++ NOW PROCESSING…
Tri M. Le
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Using BWA to create input BAM files for downstream analysis

I have Illumina paired-end reads for E. coli that I used to create a draft assembly (SPAdes). I now have the task of creating the input BAM files that I will use with Pilon -- which is used to improve a draft assembly. I decided to employ BWA using…
cer
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Plink Error while converting to binary: Line 1 of .ped file has fewer tokens than expected

Can I get some help here? Has anyone experienced the following error in plink (Whole genome association analysis toolset) while converting from 'ped','map' format to the binary counterpart 'bed','bim','fam'? I am using Linux and plink…
Daniel Fernandes
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Performance impacts of different ways to perform genetic operations on the genome of a multivariable genetic algorithm

I use genetic algorithms in my research a lot and i ran across an interesting question about how best to perform your genetic operations on a genome. Say you have a function defined by f(x,y) = ax^n + bx^n-1 + ... + cy^m + dy^m-1 ... etc. its just a…
Grant Williams
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