bowtie2_samtools

[m4gold]

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]

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]

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