User: emilyc

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emilyc10
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Posts by emilyc

<prev • 25 results • page 1 of 3 • next >
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How do I get all sequences for one specific domain from Hmmer vs Pfam output that contains the results of many domains ?
... Hello, Is there a simple way of extracting all sequences for a specific domains from hmmer vs Pfam results ? I have used esl-reformt to output the fasta containing the sequence for each domain found in my input, however it doesn't specify the domain of each sequence. Many domains were found in t ...
domain hmmer pfam written 8 days ago by emilyc10 • updated 8 days ago by Mensur Dlakic5.8k
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Comment: C: Unable to run 'pdflatex'
... Yup! I've got a LaTeX distribution installed. I could find a solution to doing this another way, but I am most interested in understanding why it won't work. After testing examples it seems that it will work on package example, but not my sequence alignment. Not certain why. ...
written 10 months ago by emilyc10
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Unable to run 'pdflatex'
... Hi everyone, I am using Rstudio for this at the moment. It appears that pdflatex won't function with msaPrettyPrint picorna = readDNAStringSet("/home/emily/pipe/RNA_merge/SPAdes/RNA_merge_picorna_of_interest.fasta") picorna_seq = paste(picorna) picorna_name = names(picorna) pico ...
R latex written 10 months ago by emilyc10
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Comment: C: Why won't this list of strings store as a variable in R?
... yes, I tried in the terminal directly. The same issue occurs. I can shorten it and get it to work also, but I was hoping to avoid having to do this. Thanks for the help! ...
written 11 months ago by emilyc10
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Comment: C: Why won't this list of strings store as a variable in R?
... Ah it's by characters - that makes more sense. Awesome, thank you! ...
written 11 months ago by emilyc10
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Comment: C: Why won't this list of strings store as a variable in R?
... Do you have any idea of the actual limit? Based on this I can manipulate it outside of R. Thanks either way. ...
written 11 months ago by emilyc10
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Comment: C: Why won't this list of strings store as a variable in R?
... Yes, it's a separate file completely manipulated in unix, none of it is manual. I've copied and pasted it into R just because I am sending this complete script to someone who doesn't understand how to use R. It's exactly the same in the file that I read in. ...
written 11 months ago by emilyc10
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Why won't this list of strings store as a variable in R?
... Hello/bonjour, I really cannot figure out the reason I am getting an error with the below when executed in R. RNA1 <- c("ARE85692.1", "WP_030538461.1", "OLA28585.1", "WP_030092979.1", "WP_011255103.1", "WP_037470143.1", "WP_037470142.1","WP_048575187.1", "WP_040265129.1", "WP_112366619.1", ...
R strings written 11 months ago by emilyc10
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Answer: A: Best command line ORF finder
... [GeneMark][1] (many options for different needs). [1]: http://topaz.gatech.edu/GeneMark/license_download.cgi ...
written 11 months ago by emilyc10
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Comment: C: InterProScan java issue
... Thank you. I am getting the following now. OpenJDK 64-Bit Server VM warning: Option AggressiveOpts was deprecated in version 11.0 and will likely be removed in a future release. Unrecognized VM option 'UseFastAccessorMethods' Error: Could not create the Java Virtual Machine. Error: ...
written 11 months ago by emilyc10

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Popular Question 9 months ago, created a question with more than 1,000 views. For Trimmomatic "no such file or directory" error with reverse input

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