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wzthu / Rbowtie2

Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval
https://www.bioconductor.org/packages/release/bioc/html/Rbowtie2.html
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bowtie2_samtools #4

Open m4gold opened 2 years ago

m4gold commented 2 years ago

Hi,

First of all thanks for developing this package (hope to use it soon!). I have been trying to familiarize myself with the package, and while trying to run the 'introduction' code from the bioconductor page, the code stops at the 'bowtie2_samtools' function which seems to be missing. While it may be embedded and used within the 'bowtie2' function it cannot be called directly.

Thanks in advance, Micah

wzthu commented 2 years ago

Hi,

bowtie2_samtools depends on the installed samtools so we do not show it in vignettes. You can follow the manual to use this function [https://bioconductor.org/packages/release/bioc/manuals/Rbowtie2/man/Rbowtie2.pdf(https://bioconductor.org/packages/release/bioc/manuals/Rbowtie2/man/Rbowtie2.pdf)

Zheng

m4gold commented 2 years ago

Thanks Zheng for the quick reply.

I am a novice to programming, so this issue may seem trivial to you. It seems that several other functions listed in manual are missing from the package installed on R (screenshot), despite having both samtools and Rsamtools installed. How would I go about troubleshooting this to see why these functions are missing?

Thanks again, Micah

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