User: wangdp123
wangdp123 • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- Oxford
- Last seen:
- 2 days, 4 hours ago
- Joined:
- 4 years, 5 months ago
- Email:
- w********@gmail.com
Posts by wangdp123
<prev
• 85 results •
page 1 of 9 •
next >
0
votes
0
answers
43
views
0
answers
... Hi there,
I am attempting to use PLINK2 with its --extract flag to extract the specific set of variants from UK Biobank dataset in *.bgen format. Unfortunately, the variant IDs contained in .bgen file is in rs_id format, which is not unique.
For example, the two different SNPs happening in the sam ...
written 2 days ago by
wangdp123 • 240
2
votes
1
answer
151
views
1
answer
... Hi there,
We are planning some proteomics experiments and I have the following two concerns regarding the replicate samples:
1) What are the minimum numbers of biological replicates (from different subjects) and technical replicates (from the same subject but run multiple times) respectively?
2) ...
0
votes
0
answers
114
views
0
answers
... Hi there,
I am looking for some best tools for calculating a variety of codon bias metrics such as RSCU, ENc, CodonO and CAI.
The input data would be a bunch of sequences from numerous genomes.
I have been aware of something like CodonW, GCUA and INCA. However, it seems that those tools have not ...
written 12 weeks ago by
wangdp123 • 240
0
votes
1
answer
103
views
1
answer
... Hi there,
I wonder if there is a smart way to retrieve the codon tables for all sequences from all contigs/scaffolds/chromosomes for all genomes from Ensembl and EnsemblGenomes databases. I suppose that all sequences from this same chromosome share the same codon table. Consequently, the question m ...
written 3 months ago by
wangdp123 • 240
• updated
3 months ago by
Ben_Ensembl • 1.5k
1
vote
1
answer
197
views
1
answer
... Hi there,
I am reading through the manual of DESeq2 package and I have run into two questions about how to use this package properly.
1) In order to perform the variance stabilising transformation, there are two ways of doing this.
i) vsd <- vst(dds, blind=TRUE)
ii) vsd <- vst(dds, ...
6
votes
0
answers
250
views
5 follow
0
answers
... Hi there,
I am looking for somewhere to run the analysis with run time of 96 hours and high memory of 800G for a short period of time.
Is there any free of charge HPC service for running this?
Any suggestion is welcome.
Many thanks,
Tom
...
0
votes
0
answers
224
views
0
answers
... Hi there,
I am using CIRCexplorer2 to annotate circRNAs from the paired-end RNA-Seq datasets and obtain a file named "circularRNA_known.txt" with the column of number of junction reads.
1) What is the cutoff to defined the expressed circRNAs according to the number of junction reads of each annota ...
written 4 months ago by
wangdp123 • 240
0
votes
1
answer
246
views
1
answers
Comment:
C: The error generated by Rsamtools
... @HD VN:1.0 SO:unsorted
@SQ SN:22 LN:50818468
@PG ID:subread PN:subread VN:Rsubread 1.34.7 CL:"subread-align" "-r" "sample.R1.fastq.gz" "-R" "sample.R2.fastq.gz" "-o" "sample.bam" "-i" "index" "--type" "0" "-n" "10" "-m" "3" "-p" "1" "-M" "3" "-T" "1" "-I" "5 ...
0
votes
1
answer
246
views
1
answers
Comment:
C: The error generated by Rsamtools
... OK. I have run the command line: `samtools quickcheck -vvv sample.bam`
The output is below:
verbosity set to 3
checking sample.bam
opened sample.bam
sample.bam is sequence data
sample.bam has 1 targets in header
sample.bam has good EOF block ...
0
votes
1
answer
246
views
1
answers
Comment:
C: The error generated by Rsamtools
... I run the following command line on terminal:
samtools quickcheck -v sample.bam
The output is empty.
...
written 5 months ago by
wangdp123 • 240
Latest awards to wangdp123
Great Question
10 weeks ago,
created a question with more than 5,000 views.
For The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question
3 months ago,
created a question with more than 1,000 views.
For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Student
3 months ago,
asked a question with at least 3 up-votes.
For Which genome fasta file and GTF file to be used in the RNA-Seq analysis
Popular Question
4 months ago,
created a question with more than 1,000 views.
For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Interproscan get stuck in "90% completed"
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Great Question
5 months ago,
created a question with more than 5,000 views.
For How to find the hub genes in the gene co-expression network constructed by WGCNA
Popular Question
5 months ago,
created a question with more than 1,000 views.
For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Interproscan get stuck in "90% completed"
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Great Question
12 months ago,
created a question with more than 5,000 views.
For The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
12 months ago,
created a question with more than 1,000 views.
For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
15 months ago,
created a question with more than 1,000 views.
For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
20 months ago,
created a question with more than 1,000 views.
For What is the difference between single-cell RNA-Seq and typical RNA-Seq in terms of data analysis procedure
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1393 users visited in the last hour