User: qwzhang0601

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qwzhang060160
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Posts by qwzhang0601

<prev • 60 results • page 1 of 6 • next >
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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 4 weeks 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 4 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 4 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 4 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 5 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 6 months ago by qwzhang060160 • updated 6 months ago by Charles Plessy2.5k
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find pseudogenes for a new genome annotation
... Hello: Recently, we assembled a new rodent species and did the genome annotation. We found several gene families are under expansion in the new species. We want to check whether the gene copies in the expanded gene families are pseudogenes or not. I looked at the PseudoPipe (i.e., an automated pseu ...
pseudogenes written 8 months ago by qwzhang060160
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Comment: C: choose the results using different parameters for CAFE3.0 (gene family expansion
... In my phylogenetic tree, there are rodent species and primates. So I just simply consider the rodent species have the same lambda, and the primates species have another lambda. When I were setting the two lambda, I am considering different branches (primate and rodent) in the same tree. thanks ...
written 9 months ago by qwzhang060160
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choose the results using different parameters for CAFE3.0 (gene family expansion analysis)
... Hello: I am using the CAFE3 to identify gene family expansion/contraction in a rodent species that I am studying. I used "caferror.py" to search the error model and get the following score. Score with global errormodel: 216055.690765 As you may know, when we use "caferror.py" to estimate the er ...
gene family contraction cafe gene family expansion written 9 months ago by qwzhang060160 • updated 9 months ago by Ben Fulton50
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From phylogenetic tree to a time tree
... Hello: I have generated a phylogenetic tree among some rodent species using single-copy protein sequences (by the method RAxML). I wonder how can I get a time tree based on the phylogenetic tree? What tools I can use, and what kind of parameters I should pay attention to? Thanks ...
raxml written 10 months ago by qwzhang060160

Latest awards to qwzhang0601

Popular Question 4 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 4 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 4 months ago, created a question with more than 1,000 views. For Prepare gene families for CAFE
Popular Question 11 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9

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