User: lauren.fitch

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Posts by lauren.fitch

<prev • 16 results • page 1 of 2 • next >
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Answer: A: ShortRead Error message: invalid character '
... The invalid character was a space. I was reading simulated FASTQs from PBSIM and it created some reads with spaces. Leaving this up in case it's helpful for anyone else. ...
written 5 weeks ago by lauren.fitch0
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ShortRead Error message: invalid character '
... Hi, I am trying to read a series of FASTQ files into R with the `ShortRead` package. It reads the first four files fine but gives an error on the fifth: ``` > test <- readFastq(buddy.file.list[[5]]) Error: Input/Output file(s): /sbgenomics/project-files/_5_buddy_0001.fastq message: in ...
shortread fastq written 5 weeks ago by lauren.fitch0
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Comment: C: Rsubread CIGAR output M only?
... Thanks, that's helpful! ...
written 6 weeks ago by lauren.fitch0
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Rsubread CIGAR output M only?
... I have been using Rsubread to map reads to a short reference sequence (amplicon sequencing). The output CIGARs are in the M format rather than the X/= format. Is it possible to get Rsubread to report mismatches with X? Thank you! Looks like this: ``` > cigar(bam.ms) [1] "239M11S" "250M" ...
rsubread cigar written 6 weeks ago by lauren.fitch0 • updated 6 weeks ago by Gordon Smyth39k
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Comment: C: Display BrowseSeqs output in R Notebook?
... Thanks! I'm creating reports for wet lab scientists at my company and it's very helpful to reduce the number of files they need to view. ...
written 10 weeks ago by lauren.fitch0
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Display BrowseSeqs output in R Notebook?
... I have been using `BrowseSeqs` from the `DECIPHER` package to view sequence alignments during analysis. The two output options are to open a browser window or save an HTML file. It would be very useful to have the results display in the R Notebook. Is there any way to do this? ...
decipher rmarkdown browseseqs notebook written 10 weeks ago by lauren.fitch0 • updated 10 weeks ago by Erik Wright140
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Comment: A: BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
... Is registration still open? The link on the bioconductor site is not working. (Sorry for the multiple posts, my boss said I can only go if I get the early bird pricing!) ...
written 2.4 years ago by lauren.fitch0
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(Closed) BioC Conference Registration Closed?
... On the main page it says "registration open!" But when you click on the link it says that registrations are not being accepted. Is the conference full? ...
bioc2017 written 2.4 years ago by lauren.fitch0
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Comment: C: Error in cleanContrast
... Sometimes you just need another pair of eyes - thank you! ...
written 3.0 years ago by lauren.fitch0
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Comment: C: Error in cleanContrast
... I was able to run the contrast successfully using this code. I'm still not sure why the original doesn't work, though.   > resultsNames(dds) [1] "Intercept" "groupHDGSE86" "groupHDGSE87" "groupHDSGSE85" > res <- results(dds, contrast = c(0, -1, 0, 1)) > ...
written 3.0 years ago by lauren.fitch0

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Popular Question 12 months ago, created a question with more than 1,000 views. For Error in cleanContrast

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