User: k.e.pendleton

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Posts by k.e.pendleton

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Comment: C: Tophat not installing with Biostar Handbook
... This is correct. Also, I didn't realize that there's a GitHub page especially for the book, so I'll try to target that instead if I think it's a book specific issue. I had also posted the question there since I thought it might be more appropriate, and I essentially got the same response. https://g ...
written 3 months ago by k.e.pendleton20
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Comment: C: Tophat not installing with Biostar Handbook
... That's cool. If I were doing real analysis, that would matter. I'm just trying to learn basics and follow the book. Thanks for the input, though. ...
written 3 months ago by k.e.pendleton20
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Tophat not installing with Biostar Handbook
... I'm working from the Biostar Handbook and trying to do the alignment with tophat. I'm on page 480 for reference. I was able to successfully run $ bowtie2-build $REF $IDX However, then it says that I need to change the invocation of the aligner to $ tophat -G $GTF -o tophat_hbr1 $IDX $R1 ...
tophat blast from the past: the tuxedo suite written 3 months ago by k.e.pendleton20 • updated 3 months ago by h.mon16k
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Comment: C: Bioconductor not working through Unix command line
... Ah. Thanks! I'll try to keep this in mind. I struggle looking for solutions to some easy issues since I don't have the right language yet to properly say what's going wrong. ...
written 3 months ago by k.e.pendleton20
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Comment: C: Bioconductor not working through Unix command line
... Just for future reference if anyone ever has this issue, I've mostly fixed it now. For some reason, bash thinks R is in one place, even though it also knows it's in another. I don't really get it. ANYWAY. If I run the command where it specifies Rscript in the correct place: $ cat counts.txt | ...
written 3 months ago by k.e.pendleton20
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Comment: C: Bioconductor not working through Unix command line
... So, it turns out that I'm just impatient, and R did download. I have good and bad news. When I try to run the Rscript in command line, it still fails. $ cat counts.txt | Rscript deseq1.r 3x3 > results_deseq1.txt bash: /usr/bin/Rscript: No such file or directory (bioinfo) $ ...
written 4 months ago by k.e.pendleton20
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Comment: C: Bioconductor not working through Unix command line
... $ which Rscript /home/moltres/miniconda3/envs/bioinfo/bin/Rscript Okay. How do I know if it's from anaconda? Is it in the wrong directory? Thanks for the response. Still trying to figure this out. Also, if it counts for anything I tried to uninstall everything. I did... $ sudo apt-ge ...
written 4 months ago by k.e.pendleton20
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Bioconductor not working through Unix command line
... I'm working through the Bioconductor book and am currently int he RNA-Seq statistics: R and Bioconductor section. I've actually used both R and Bioconductor before, but in Windows, not Linux. I have R installed. If I try to run conda install r again, everything freezes up and I have to open up anot ...
R rna-seq statistics: r and bioconductor written 4 months ago by k.e.pendleton20 • updated 4 months ago by Sean Davis24k

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