Moderator: karl.stamm

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karl.stamm3.8k
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Posts by karl.stamm

<prev • 504 results • page 1 of 51 • next >
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Comment: C: Genes inhibiting each other's expression
... Underrepresented in the networks people have inferred or constructed. Hidden phenomena are hidden. ...
written 7 days ago by karl.stamm3.8k
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Comment: C: Why are we assuming most genes are not differentially expressed?
... Dariober's answer is a good one for the followup question: assuming most genes are not DE, then how can we solve many of the false-positives generated by technical processes like library amplification and sequencing. If I recall correctly there's another good discussion of this method in the DESeq2 ...
written 13 days ago by karl.stamm3.8k
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Answer: A: Why are we assuming most genes are not differentially expressed?
... The assumption comes from the experimental design: We're testing similar samples with just the experimental factor changed. Should be the same kind of mice, with or without a drug treatment. Or the same kind of corn with or without extra irrigation. Consider the converse: If you were to rna-seq a ...
written 13 days ago by karl.stamm3.8k
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Comment: C: How to deal with two gene sets have exact same values from GSVA results?
... What's the problem? It's not clear what you're trying to do. ...
written 13 days ago by karl.stamm3.8k
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Comment: C: How to answer dis?
... Hello Voyboy488! We believe that this post does not fit the main topic of this site. Low effort homework post. We cannot do your homework. Biostars is an informational Q&A site. If you have a question please search for it in our history, or ask it clearly so it can be answered. For this reas ...
written 17 days ago by karl.stamm3.8k
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Comment: C: Does 1000 genomes have a flat file with allele frequencies for each site anywher
... ANNOVAR had compiled something like that, you could install it and pull the datafiles out. ...
written 22 days ago by karl.stamm3.8k
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Comment: C: Resources for learning how to submit jobs in unix-based cluster
... Your cluster could be running any number of queuing or workload softwares. Get in touch with the administrators, they will have guidelines. At least they can say "we run qsub" or "we run slurm" then you can Google how to use that tool. ...
written 22 days ago by karl.stamm3.8k
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Comment: C: Reviewing some of these answers from bioinformatics lab
... First thought: you will get some negativity as we are generally against doing others' homework. but you were forthright that this is open for discussion and not just asking us the answers, so I see no harm. so I'm a computationalist, we would more often take other's formulas and run them, I dont ...
written 27 days ago by karl.stamm3.8k
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Comment: C: rnammer error :the command line on the script does not work
... As I said, it probably has more problems within the script, now you've got "bad interpreter: No such file or directory" and we've fixed the original error of permission Denied. Moving the file "from Trinotate" gave you a funny/broken edition. ...
written 5 weeks ago by karl.stamm3.8k
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Comment: C: rnammer error :the command line on the script does not work
... The error says permission denied. That's your operating system saying No to running that command. The file is not executable, or the folder is restricted. I'm tempted to say this isn't a bio-informatics issue at all, but a simple sysadmin issue. Not Mummer's fault your system setup is incomplete. B ...
written 5 weeks ago by karl.stamm3.8k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Not sure how to go about creating the "mylist.txt" file for the --update
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Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
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