User: jyu429

gravatar for jyu429
jyu429120
Reputation:
120
Status:
Trusted
Location:
United States
Last seen:
1 year, 1 month ago
Joined:
4 years, 3 months ago
Email:
j*****@gmail.com

Posts by jyu429

<prev • 36 results • page 1 of 4 • next >
0
votes
1
answer
436
views
1
answer
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 14 months ago by jyu429120 • updated 13 months ago by Brian Gudenas90
0
votes
1
answer
1.6k
views
1
answers
Comment: C: Problems installing ete3 using conda
... No, I don't think so. ...
written 24 months ago by jyu429120
2
votes
1
answer
1.6k
views
1
answer
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 24 months ago by jyu429120 • updated 22 months ago by Madhuran Thiagarajah0
1
vote
1
answer
621
views
1
answer
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 2.0 years ago by jyu429120 • updated 23 months ago by Biostar ♦♦ 20
0
votes
1
answer
974
views
1
answer
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 2.1 years ago by jyu429120 • updated 19 months ago by lloydlow0
0
votes
1
answer
779
views
1
answer
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 2.4 years ago by jyu429120 • updated 2.4 years ago by vakul.mohanty240
3
votes
1
answer
732
views
1
answer
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 2.5 years ago by jyu429120 • updated 2.5 years ago by igor7.3k
0
votes
0
answers
1.4k
views
0
answers
Comment: C: Merging bam files
... I updated it and it gives me the same error.  ...
written 3.2 years ago by jyu429120
0
votes
0
answers
1.4k
views
0
answers
Comment: A: Merging bam files
... Version 1.1. Is that too outdated? ...
written 3.2 years ago by jyu429120
5
votes
0
answers
1.4k
views
0
answers
Merging bam files
... 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 ...
merge bam written 3.2 years ago by jyu429120

Latest awards to jyu429

Popular Question 23 months ago, created a question with more than 1,000 views. For IgBlast installation from src files
Popular Question 23 months ago, created a question with more than 1,000 views. For Filtering fasta file based on identifier
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Filtering fasta file based on identifier
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Understanding bowtie2 output

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1261 users visited in the last hour