User: wangdp123

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wangdp123240
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Oxford
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Posts by wangdp123

<prev • 85 results • page 1 of 9 • next >
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Use PLINK2 to extract the specific variants
... 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 ...
plink2 written 2 days ago by wangdp123240
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The number of biological replicates and technical replicates in proteomics experiments
... 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) ...
proteomics replicates written 10 weeks ago by wangdp123240 • updated 10 weeks ago by JC10k
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Codon bias calculation tool
... 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 ...
codon bias written 12 weeks ago by wangdp123240
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The codon table for all contigs/scaffolds/chromosomes of all genomes from Ensembl databases
... 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 ...
ensembl codon written 3 months ago by wangdp123240 • updated 3 months ago by Ben_Ensembl1.5k
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Some questions regarding DESeq2
... 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, ...
deseq2 rna-seq written 4 months ago by wangdp123240 • updated 4 months ago by dsull1.4k
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Forum: A free temporary HPC service for bioinformatic analysis
... 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 ...
hpc forum written 4 months ago by wangdp123240 • updated 4 months ago by h.mon30k
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Perform differential circular RNA expression
... 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 ...
circexplorer2 circrna written 4 months ago by wangdp123240
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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 ...
written 5 months ago by wangdp123240 • updated 5 months ago by RamRS28k
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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 ...
written 5 months ago by wangdp123240 • updated 5 months ago by RamRS28k
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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 wangdp123240

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"
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"
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 KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
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

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