How To Install R-Rsolid on Fedora 36

In this tutorial we learn how to install R-Rsolid in Fedora 36. R-Rsolid is Quantile normalization and base calling for second generation sequencing data

Introduction

In this tutorial we learn how to install R-Rsolid on Fedora 36.

What is R-Rsolid

Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance.

We can use yum or dnf to install R-Rsolid on Fedora 36. In this tutorial we discuss both methods but you only need to choose one of method to install R-Rsolid.

Install R-Rsolid on Fedora 36 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

After updating yum database, We can install R-Rsolid using dnf by running the following command:

sudo dnf -y install R-Rsolid

Install R-Rsolid on Fedora 36 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

After updating yum database, We can install R-Rsolid using yum by running the following command:

sudo yum -y install R-Rsolid

How To Uninstall R-Rsolid on Fedora 36

To uninstall only the R-Rsolid package we can use the following command:

sudo dnf remove R-Rsolid

R-Rsolid Package Contents on Fedora 36

/usr/lib/.build-id
/usr/lib/.build-id/a3
/usr/lib/.build-id/a3/c0e833543eec5d5fe7366ca1ce78b045f7deb4
/usr/lib/R/library/Rsolid
/usr/lib/R/library/Rsolid/DESCRIPTION
/usr/lib/R/library/Rsolid/INDEX
/usr/lib/R/library/Rsolid/Meta
/usr/lib/R/library/Rsolid/Meta/Rd.rds
/usr/lib/R/library/Rsolid/Meta/data.rds
/usr/lib/R/library/Rsolid/Meta/features.rds
/usr/lib/R/library/Rsolid/Meta/hsearch.rds
/usr/lib/R/library/Rsolid/Meta/links.rds
/usr/lib/R/library/Rsolid/Meta/nsInfo.rds
/usr/lib/R/library/Rsolid/Meta/package.rds
/usr/lib/R/library/Rsolid/NAMESPACE
/usr/lib/R/library/Rsolid/R
/usr/lib/R/library/Rsolid/R/Rsolid
/usr/lib/R/library/Rsolid/R/Rsolid.rdb
/usr/lib/R/library/Rsolid/R/Rsolid.rdx
/usr/lib/R/library/Rsolid/data
/usr/lib/R/library/Rsolid/data/prop.Hs.rda
/usr/lib/R/library/Rsolid/help
/usr/lib/R/library/Rsolid/help/AnIndex
/usr/lib/R/library/Rsolid/help/Rsolid.html
/usr/lib/R/library/Rsolid/help/Rsolid.rdb
/usr/lib/R/library/Rsolid/help/Rsolid.rdx
/usr/lib/R/library/Rsolid/help/aliases.rds
/usr/lib/R/library/Rsolid/help/paths.rds
/usr/lib/R/library/Rsolid/html
/usr/lib/R/library/Rsolid/html/00Index.html
/usr/lib/R/library/Rsolid/html/R.css
/usr/lib/R/library/Rsolid/html/Rsolid.html
/usr/lib/R/library/Rsolid/libs
/usr/lib/R/library/Rsolid/libs/Rsolid.so

References

Summary

In this tutorial we learn how to install R-Rsolid on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).

title: “How To Install R-Rsolid on Fedora 36” linkTitle: “R-Rsolid” type: “docs” description: “In this tutorial we learn how to install R-Rsolid in Fedora 36. R-Rsolid is Quantile normalization and base calling for second generation sequencing data” date: “2022-08-17” lastmod: “2022-08-17” #image: /images/fedora/36/R-Rsolid-featured.png

Introduction

In this tutorial we learn how to install R-Rsolid on Fedora 36.

What is R-Rsolid

Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance.

We can use yum or dnf to install R-Rsolid on Fedora 36. In this tutorial we discuss both methods but you only need to choose one of method to install R-Rsolid.

Install R-Rsolid on Fedora 36 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

After updating yum database, We can install R-Rsolid using dnf by running the following command:

sudo dnf -y install R-Rsolid

Install R-Rsolid on Fedora 36 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

After updating yum database, We can install R-Rsolid using yum by running the following command:

sudo yum -y install R-Rsolid

How To Uninstall R-Rsolid on Fedora 36

To uninstall only the R-Rsolid package we can use the following command:

sudo dnf remove R-Rsolid

R-Rsolid Package Contents on Fedora 36

/usr/lib/.build-id
/usr/lib/.build-id/6c
/usr/lib/.build-id/6c/99d5462d857f75bc1d04a8355895b06503e1db
/usr/lib64/R/library/Rsolid
/usr/lib64/R/library/Rsolid/DESCRIPTION
/usr/lib64/R/library/Rsolid/INDEX
/usr/lib64/R/library/Rsolid/Meta
/usr/lib64/R/library/Rsolid/Meta/Rd.rds
/usr/lib64/R/library/Rsolid/Meta/data.rds
/usr/lib64/R/library/Rsolid/Meta/features.rds
/usr/lib64/R/library/Rsolid/Meta/hsearch.rds
/usr/lib64/R/library/Rsolid/Meta/links.rds
/usr/lib64/R/library/Rsolid/Meta/nsInfo.rds
/usr/lib64/R/library/Rsolid/Meta/package.rds
/usr/lib64/R/library/Rsolid/NAMESPACE
/usr/lib64/R/library/Rsolid/R
/usr/lib64/R/library/Rsolid/R/Rsolid
/usr/lib64/R/library/Rsolid/R/Rsolid.rdb
/usr/lib64/R/library/Rsolid/R/Rsolid.rdx
/usr/lib64/R/library/Rsolid/data
/usr/lib64/R/library/Rsolid/data/prop.Hs.rda
/usr/lib64/R/library/Rsolid/help
/usr/lib64/R/library/Rsolid/help/AnIndex
/usr/lib64/R/library/Rsolid/help/Rsolid.html
/usr/lib64/R/library/Rsolid/help/Rsolid.rdb
/usr/lib64/R/library/Rsolid/help/Rsolid.rdx
/usr/lib64/R/library/Rsolid/help/aliases.rds
/usr/lib64/R/library/Rsolid/help/paths.rds
/usr/lib64/R/library/Rsolid/html
/usr/lib64/R/library/Rsolid/html/00Index.html
/usr/lib64/R/library/Rsolid/html/R.css
/usr/lib64/R/library/Rsolid/html/Rsolid.html
/usr/lib64/R/library/Rsolid/libs
/usr/lib64/R/library/Rsolid/libs/Rsolid.so

References

Summary

In this tutorial we learn how to install R-Rsolid on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).