User: jyu429
jyu429 • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 3 months ago
- Joined:
- 4 years, 7 months ago
- Email:
- j*****@gmail.com
Posts by jyu429
<prev
• 38 results •
page 1 of 4 •
next >
0
votes
0
answers
152
views
0
answers
... Is that really faster than for example implementing a search trie? ...
written 3 months ago by
jyu429 • 120
0
votes
0
answers
152
views
0
answers
... 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! ...
0
votes
1
answer
512
views
1
answer
... 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 18 months ago by
jyu429 • 120
• updated
17 months ago by
Brian Gudenas • 90
0
votes
1
answer
1.9k
views
1
answers
... No, I don't think so. ...
written 2.3 years ago by
jyu429 • 120
2
votes
1
answer
1.9k
views
1
answer
... 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 2.3 years ago by
jyu429 • 120
• updated
2.2 years ago by
Madhuran Thiagarajah • 0
1
vote
1
answer
712
views
1
answer
... 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 ...
0
votes
1
answer
1.1k
views
1
answer
... 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 ...
0
votes
1
answer
856
views
1
answer
... 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 2.7 years ago by
jyu429 • 120
• updated
2.7 years ago by
vakul.mohanty • 240
3
votes
1
answer
804
views
1
answer
... 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! ...
0
votes
0
answers
1.5k
views
0
answers
Comment:
C: Merging bam files
... I updated it and it gives me the same error.
...
written 3.5 years ago by
jyu429 • 120
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1512 users visited in the last hour