miRNAbowtieRun: Primary mapping of short reads with Bowtie/Picard for miRNA
In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
Description
A function for primary mapping of short reads with bowtie and the conversion of the SAM output into BAM format
In the actual implementation it is possible to run bowtie using single-end fastq files produced using Illumina platform.
The available reference sets are derived by miRbase precursors and are available for human, hs, mouse, mm, rat, rn, and bovine, bo.
It is strongly suggested to run a trimming of the 3 and 5 end linkers before performing the mapping with bowtie.
In the present implementation bowtie runs with the following parameters: -a –best -k 1 -q -v 3 -S. Therefore only the first best alignment is
shown, imput files are in fastq format, alingement up to three mismatches are considered and the output is in SAM format.
At the end of the mapping SAM files are converted in BAM files using picard tools.
Usage
1
Author(s)
Raffaele A Calogero
oneChannelGUI documentation built on Nov. 17, 2017, 11:02 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
A function for primary mapping of short reads with bowtie and the conversion of the SAM output into BAM format In the actual implementation it is possible to run bowtie using single-end fastq files produced using Illumina platform. The available reference sets are derived by miRbase precursors and are available for human, hs, mouse, mm, rat, rn, and bovine, bo. It is strongly suggested to run a trimming of the 3 and 5 end linkers before performing the mapping with bowtie. In the present implementation bowtie runs with the following parameters: -a –best -k 1 -q -v 3 -S. Therefore only the first best alignment is shown, imput files are in fastq format, alingement up to three mismatches are considered and the output is in SAM format. At the end of the mapping SAM files are converted in BAM files using picard tools.
Usage
1 |
Author(s)
Raffaele A Calogero
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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