User: jyu429

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jyu429120
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3 months ago
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4 years, 7 months ago
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Posts by jyu429

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Finding all positions for all kmers belonging to a (not so short) list of kmers
... Is that really faster than for example implementing a search trie? ...
written 3 months ago by jyu429120
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Finding all positions for all kmers belonging to a (not so short) list of kmers in a large genome
... Hi, Is there a tool for not only enumerating the counts of kmers (like jellyfish) but also will list their positions? I know its much more exhausting memory-wise but I'm looking for the best way to do this, even if a tool doesn't exist currently. Thanks! ...
genome kmer sequencing written 3 months ago by jyu429120 • updated 3 months ago by ATpoint17k
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Download all files from encode matching filter specifications
... Hi, I'm wondering how I might go about downloading all the files and associated summary information from encodeproject.org that match a specific set of filters. For example, if I want Assay: ChiP-seq Genome assembly: GRCh38 Organism: Homo sapiens Target of assay: histone, recombinant protein O ...
encode written 18 months ago by jyu429120 • updated 17 months ago by Brian Gudenas90
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Comment: C: Problems installing ete3 using conda
... No, I don't think so. ...
written 2.3 years ago by jyu429120
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Problems installing ete3 using conda
... Hi, I'm having some trouble installing ete3 using the recommended conda way. I first ran `conda install -y pip six numpy pyqt lxml gcc` to install all the dependencies, but then when I ran `conda install -c etetoolkit ete3 ete3_external_apps` I was met with this error: UnsatisfiableError: The ...
ete3 conda written 2.3 years ago by jyu429120 • updated 2.2 years ago by Madhuran Thiagarajah0
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Using ete3 without knowing tree topology
... Hi, I would like to start using ETE Toolkit (http://etetoolkit.org/) for creating a phylogenetic tree from DNA sequences from severla human individuals. I already have the alignment, but it seems like you have to specify and know the topology of the tree beforehand. Is there a way to infer the topo ...
ete3 phylogenetic tree written 2.3 years ago by jyu429120 • updated 2.3 years ago by Biostar ♦♦ 20
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HapCUT2 using GATK results
... Hi, I'm trying to generate haplotypes from using both WGS reads from a bam file and GATK results identifying unphased variants as a vcf. I was considering using HapCUT2, but the vcf format required as input (as detailed [here][1]) seems to be significantly different from the vcf format that GATK ou ...
hapcut2 gatk vcf phasing written 2.4 years ago by jyu429120 • updated 23 months ago by lloydlow0
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GATK allele frequencies
... Hi, I'm using the GATK Haplotype caller to call for variants, but I'd like to output the genotype fields. For this, I believe I have to use the -GF option, but is this an incorrect way? > java -jar $HOME/Tools/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -GF -T > HaplotypeCaller -R "imgt_VH_fil ...
gatk allele frequency written 2.7 years ago by jyu429120 • updated 2.7 years ago by vakul.mohanty240
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Paired end FASTA to single BAM file
... Hi, I'm interested in taking two fastq files X_1.fq and X_2.fq creating a single bam file X.bam, unmapped to anything. Is there a way to do this with just bowtie2 and samtools? Thank you for the help! ...
samtools written 2.8 years ago by jyu429120 • updated 2.8 years ago by igor7.7k
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Comment: C: Merging bam files
... I updated it and it gives me the same error.  ...
written 3.5 years ago by jyu429120

Latest awards to jyu429

Popular Question 18 months ago, created a question with more than 1,000 views. For Merging bam files
Popular Question 18 months ago, created a question with more than 1,000 views. For IgBlast installation from src files
Popular Question 18 months ago, created a question with more than 1,000 views. For All sam flags specifying first mate?
Popular Question 18 months ago, created a question with more than 1,000 views. For simulate reads with zero mutations
Popular Question 18 months ago, created a question with more than 1,000 views. For bowtie2 --score-min how to input function
Popular Question 18 months ago, created a question with more than 1,000 views. For Filtering fasta file based on identifier
Popular Question 18 months ago, created a question with more than 1,000 views. For Piping samtools commands
Popular Question 18 months ago, created a question with more than 1,000 views. For bioawk for identifiers that don't match pattern
Popular Question 2.3 years ago, created a question with more than 1,000 views. For IgBlast installation from src files
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Filtering fasta file based on identifier
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Filtering fasta file based on identifier
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Understanding bowtie2 output

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