User: qwzhang0601

gravatar for qwzhang0601
qwzhang060170
Reputation:
70
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Trusted
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United States
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3 weeks, 3 days ago
Joined:
5 years, 10 months ago
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Posts by qwzhang0601

<prev • 78 results • page 1 of 8 • next >
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Comment: C: TCGA raw RNA-Seq data
... Thank you. Do you know how/where can I check all TCGA lung cancer samples to get their information (e.g., sub-type, availability of RNA-Seq, mutation data, etc)? Since there will be more than hundreds of samples, I want to know some computational tools to get such information, or where to find such ...
written 24 days ago by qwzhang060170
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TCGA raw RNA-Seq data
... I want to make use of RNA-Seq data of TCGA samples to measure expression of transposes of lung cancer samples, so I would need the raw RNA-Seq data. I know TCGA moved to GDC. I wonder how can I get the data? Briefly, I want to cluster sub-types of those lung cancer samples, and check how many sample ...
tcga rna-seq written 24 days ago by qwzhang060170 • updated 24 days ago by ATpoint41k
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merge file according to IDs
... I have several files including read counts covering CpG sites, methylated and unmethylated (shown as below). Since I have tens of different samples, which have different CpG sites covered. Is there some command or R function which can merge such files easily? Merge the rows based on ChrID and positi ...
sequencing written 5 weeks ago by qwzhang060170 • updated 5 weeks ago by rpolicastro2.3k
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sum counts in regions in bed format
... I have processed the DNA methylation data and generate the file showing read count that call each CpG site as methylated or unmethylated. Now I want to sum such read counts in sliding windows. Is there some tools can do this easily? Briefly, for each window I will need to save the number of CpG site ...
sequencing written 5 weeks ago by qwzhang060170
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RNA-Seq database across rodents
... I wonder whether there are some database for gene expression of certain tissues across diverse rodent species? I know such database for mouse and rat, but not sure about other rodent species (e.g., naked mole rat, blind mole rat). We plan to do some phylogeny comparative analysis among rodents using ...
gene expression rna-seq written 4 months ago by qwzhang060170
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Answer: A: alignment with phylogenetic tree
... Thank you! Briefly, I want to show multiple sequencing alignment. Some sites under positive selection may evolve differently among different species. So I want to order the sequences according to the phylogenetic tree of those species. Thanks ...
written 15 months ago by qwzhang060170
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alignment with phylogenetic tree
... I have phylogenetic tree of 100 species, and I also have the multiple sequence alignment file for a gene we are interested in. I wonder whether there is some tool to generate a plot which shows both phylogenetic tree of the 100 species and sequence alignment of the gene from 100 species? Thanks ...
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Comment: C: obstain 100-way alignment of 100 species for a certain gene
... Thank you for your suggestion. I tried to get the alignment, but it seem it generate the alignment on the gene DNA sequence level (including noncoding part), right? I see many long gaps in the alignment. Is there a way to only include CDS sequence or protein sequence? Thanks ...
written 15 months ago by qwzhang060170
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Comment: C: obstain 100-way alignment of 100 species for a certain gene
... Thanks. I got the files (like refGene.exonAA.fa.gz) from the link you provided. But it seems, it only includes alignment on exon level. We need to merge all exons by myself. Am I right? Not sure whether there is a direct way to do this, or any tool can help to merge alignment of exons into alignmen ...
written 15 months ago by qwzhang060170
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obstain 100-way alignment of 100 species for a certain gene
... I want to get the alignment file (Amino acid for protein, and nucleotide for CDS) for a particular gene from 100-way alignment of 100 species (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz100way). Is there an easy way to get it? Thanks ...

Latest awards to qwzhang0601

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 4 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 4 months ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 4 months ago, created a question with more than 1,000 views. For orthologs between mouse and blind mole rat
Great Question 15 months ago, created a question with more than 5,000 views. For Repeatmasker, Can't locate Text/Soundex.pm
Popular Question 15 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 15 months ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 15 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 15 months ago, created a question with more than 1,000 views. For read counts for RNA-seq analysis of repeat elements
Popular Question 15 months ago, created a question with more than 1,000 views. For BUSCOs running time
Popular Question 15 months ago, created a question with more than 1,000 views. For copy number of genes
Popular Question 15 months ago, created a question with more than 1,000 views. For Reciprocal best hit by blast
Popular Question 20 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 20 months ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 20 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 20 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Browser of 1000 genome phase 3 showing allele frequency in each population
Popular Question 2.4 years ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Length of transcripts of mm9

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