User: qwzhang0601

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qwzhang060160
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2 months ago
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3 years, 11 months ago
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Posts by qwzhang0601

<prev • 64 results • page 1 of 7 • next >
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Comment: C: compare and merge VCF files
... It seems a little bit complex. But thanks. ...
written 9 weeks ago by qwzhang060160
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Comment: C: compare and merge VCF files
... Thanks!I will take a look. ...
written 9 weeks 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 9 weeks ago by qwzhang060160 • updated 8 weeks 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 3 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 6 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 9 months ago by qwzhang060160
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Comment: C: read counts for RNA-seq analysis of repeat elements
... Thank you for your suggestion. I plan to use TEtranscript, which aggregate counts over sub-families. ...
written 9 months ago by qwzhang060160
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read counts for RNA-seq analysis of repeat elements
... We are studying repeat elements in mouse (comparing samples between 2 conditions with 3 replicates each). We plan to do RNA-seq sequencing for all coding genes and repeat elements. For the reads we will do 150bp paired-end sequencing. But we are not sure how many reads are enough for the differentia ...
repeats rna-seq written 9 months ago by qwzhang060160
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Comment: C: BUSCOs running time
... Finally, I found we need to install the perl module “Parallel::ForkManager” to run optimize_augustus.pl in parallel. You can look at the "augustus.log" file, and check if you have the same problem. I found the following information in the "augustus.log" file, so I installed the "Parallel::ForkMana ...
written 10 months ago by qwzhang060160
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install genewise (wise2.4.1) on linux
... I am trying to install genewise on a linux systerm (Linux 2.6.32-696.6.3.el6.694g0000.x86_64). I have edit the files for known issues (e,g, replace "cc" by "gcc", replace "isnumber" by "isdigit", etc). But still I got the following errors. [src]$ make all (cd base ; make CC="gcc" CF ...
genewise written 11 months ago by qwzhang060160 • updated 11 months ago by Charles Plessy2.6k

Latest awards to qwzhang0601

Popular Question 6 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 6 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 6 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 6 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 9 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 9 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 9 months ago, created a question with more than 1,000 views. For Prepare gene families for CAFE
Popular Question 16 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9

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