User: jyu429
jyu429 • 120
- Reputation:
- 120
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- Location:
- United States
- Last seen:
- 1 year, 1 month ago
- Joined:
- 4 years, 3 months ago
- Email:
- j*****@gmail.com
Posts by jyu429
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... 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 ...
written 14 months ago by
jyu429 • 120
• updated
13 months ago by
Brian Gudenas • 90
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... No, I don't think so. ...
written 24 months ago by
jyu429 • 120
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1
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... 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 ...
written 24 months ago by
jyu429 • 120
• updated
22 months ago by
Madhuran Thiagarajah • 0
1
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... 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 ...
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... 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 ...
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... 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 ...
written 2.4 years ago by
jyu429 • 120
• updated
2.4 years ago by
vakul.mohanty • 240
3
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1
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732
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1
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... 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! ...
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Comment:
C: Merging bam files
... I updated it and it gives me the same error.
...
written 3.2 years ago by
jyu429 • 120
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1.4k
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Comment:
A: Merging bam files
... Version 1.1. Is that too outdated?
...
written 3.2 years ago by
jyu429 • 120
5
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1.4k
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... Hi, I'm trying to merge these two bam files and I did the command
samtools merge merged.bam file1.bam file2.bam
However, it gives me this error: [trans_tbl_init] @SQ SN (hg38_gold start=chr14:105786368 strand=+) found in binary header but not text header. I'm not sure how to get around this. Is ...
written 3.2 years ago by
jyu429 • 120
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