User: aquaq

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aquaq20
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3 months, 1 week ago
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3 years, 9 months ago
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Posts by aquaq

<prev • 25 results • page 1 of 3 • next >
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Answer: A: How to get all descendants of a GO-term OR how to identifiy if a GO-term is an a
... Finally I found: go_term.get_all_parents() would give me all parents with 'is a' relation, that is good enough for my purposes. ...
written 4 months ago by aquaq20
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How to get all descendants of a GO-term OR how to identifiy if a GO-term is an ancestor of another?
... Hi All, I am using goatools in python and I was wondering if there are any easy ways, without iteratively looping through the tree, to determine all the descendants of a GO term. Alternatively, is there a way to determine whether a GO-term is a descendant (of any level) of another GO-term? Thank y ...
goatools python go written 4 months ago by aquaq20
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Answer: A: how to retrieve the antibiotics resistance genes in the plasmid sequence
... What about using CARD? https://card.mcmaster.ca/ You can either BLAST against the database or use their Resistance gene identifier (Analyze menu). ...
written 6 months ago by aquaq20
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Comment: C: Download pnly latest sequences from GenBank
... Thank you, I would have never searched for this there :) You saved me a lot of time! ...
written 9 months ago by aquaq20
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Download pnly latest sequences from GenBank
... Hi All, I am developing a webserver that would run a pipeline at every update of GenBank. After every update, I would like to download only those sequences that were added during the last update. Is it possible to do programatically without downloading the whole database? If yes, how? Thank you fo ...
genbank written 9 months ago by aquaq20 • updated 9 months ago by Xylanaser60
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Downloading PhosphoSitePlus older versions
... Hi all, I would like to get a specific version of PhosphoSitePlus, but cannot find a link to older versions on the webpage (yes, I tried google as well). Do you know any method how to access those? I have written to the support team but has no idea how long does it take for them to answer a questio ...
ptm phosphosite version written 12 months ago by aquaq20
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Comment: C: How to run sleuth in single run mode?
... You are right, I have misread it. Thank you! ...
written 22 months ago by aquaq20
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How to run sleuth in single run mode?
... Hi! I have run kallisto on RNA-Seq data from SRA. Unfortunately, it does not have any replicates. After kallisto, I try to run sleuth with recommended commands (https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html). However, sleuth_fit gives an error the exact same as described i ...
sleuth kallisto rna-seq written 22 months ago by aquaq20
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Rna-seq: How to normalize them with biological replicates to get change ratio?
... We have a cell line with certain plasmids added. The initial sample was split into three subsamples, plus it was sequenced once. The three subsamples were grown differently, then each sequenced once (of course the four library was pooled begore sequencing with their respective barcodes added). The s ...
rna-seq written 2.7 years ago by aquaq20
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Comment: C: Why do they use ratios for differential expression analysis?
... Thanks. I was thinking on microarray and realozed that with flurescency, it might be ratio scale. However, I've read that RNA-Seq measure counts relative to the number of all reads, and absolute quantification would be possible by adding controls (spikes). ...
written 2.7 years ago by aquaq20

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to merge paired-end reads from sam files?

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