User: qwzhang0601

gravatar for qwzhang0601
qwzhang060160
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United States
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3 months, 3 weeks ago
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4 years, 5 months ago
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Posts by qwzhang0601

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Validate PCR DNA primers against whole de novel genome
... Ok. Thank you very much. ...
written 4 months ago by qwzhang060160
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Comment: C: Validate PCR DNA primers against whole de novel genome
... Many thanks. Is there a publication and manual for dicey? I am looking at MFEprimer-3.0 (https://www.mfeprimer.com/), have you tried this before? Thank you ...
written 4 months ago by qwzhang060160
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Validate PCR DNA primers against whole de novel genome
... I want to test gene copy number of some genes. I designed the primer using primer3 and what to test whether the primers are specific to my genes. I know some tools can do this. For example, I tried primer-blast, but it can not work when I test it against the whole genome (about 3G base pairs). I als ...
primers in sillico written 4 months ago by qwzhang060160 • updated 4 months ago by trausch1.3k
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Design paralog-specific primer for RT-PCR on de novel genome
... We assembled the genome of a new rodent species. We also did gene annotation. There is one gene showing expansion in our rodent genome (7 copies in our genome, 2 copies in mouse and 1 copy in human). Below show our evidence that we consider the gene are very likely under expansion. Now we want to ...
qrt-pcr primer written 5 months ago by qwzhang060160
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Comment: C: compare and merge VCF files
... It seems a little bit complex. But thanks. ...
written 8 months ago by qwzhang060160
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Comment: C: compare and merge VCF files
... Thanks!I will take a look. ...
written 8 months ago by qwzhang060160
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compare and merge VCF files
... We have SNP array data and whole exon sequencing based SNP calling results for the same group of samples. Now we have genotype data in VCF format from both techniques. The samples are the sames. But the list of SNPs can be different, with some overlapped SNPs from both data. We want to merge the V ...
vcf genotype written 8 months ago by qwzhang060160 • updated 7 months ago by berrytaylor560
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Compare gene expression in two species
... I have assembled a new rodent genome and find several genes under expansion (with more gene copies) comparing to human/mouse. I want to check whether the expanded gene show higher expression level in the rodent species comparing to human/mouse (besides, I am also interested in seeing other genes sho ...
rna-seq written 9 months ago by qwzhang060160
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is there a tool to visualize and compare gene structure of orthologs/paralogs?
... I have identified gene families among several species. I want to visualize and compare their gene structure among orthologs of different species, or paralogs within one species. Are there such tools? I already have those orthologs, their sequences and the GTF files. Thanks ...
paralog ortholog visualization written 12 months ago by qwzhang060160
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align reads to regions with similar sequences
... When we do alignment of NGS data (i.e., RNA-seq, ChIP-seq) to the genome, we usually allow certain mismatches for the alignment. Suppose we allow 2 mismatches (we also accept reads mappable to multiple loci) and a read can match to loci A of the genome with 0 mismatch, match loci B with 1 mismatch ...
alignment written 15 months ago by qwzhang060160

Latest awards to qwzhang0601

Popular Question 4 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 7 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 7 months ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 7 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 12 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 12 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 12 months 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 12 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 Length of transcripts of mm9
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 Prepare gene families for CAFE
Popular Question 22 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9

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