UMIc is a framework, written in R, implementing a new proposed method for UMI deduplication and reads correction. The method works at nucleotide level, taking into account the frequency and the mean quality of each base.
The packages needed to be installed, in order to run the project are:
- from CRAN
install.packages(c("tidyverse", "data.table", "stringr"))
- from Bioconductor
BiocManager::install(c("Biostrings", "ShortRead"))
The project can be downloaded using git:
git clone https://github.com/mcmaniou/projectUMIs
The framework consists of three scripts:
UMIsProject.R
casesWorkflows.R
functions.R
In order to run the project, use the following command:
source("UMIsProject.R")
Before running the project, the user must set the appropriate input parameters in the main script UMIsProject.R
.
The later has the following inputs:
pairedData
: boolean variable that indicates, whether data are pairedT
or singleF
.UMIlocation
: variable that indicates, whether UMI is located only in Read1R1
or Read1 and Read2R1 & R2
.UMIlength
: the length of the UMI sequence.sequenceLength
: the length of the read sequence.countsCutoff
: min read counts per UMI, for initial data cleaning.UMIdistance
: max UMI distance for UMI merging.sequenceDistance
: max sequence distance for UMI merging.inputsFolder
: name or filepath of the inputs folder.outputsFolder
: name or filepath of the outputs folder, default value isUMIc_output
.
The input data must be provided in fastq files and it is assumed that the UMI is placed at the beginning of each sequence. The library preparation step of the input files must be genarated using the same protocol and fulfil the same input parameters described above.
The output data are stored also in fastq files, named the same as the input files with an added _corrected
suffix and the name of the folder can be provided by the user. The files contain the corrected sequences (without the UMI) and their quality. It is worth mentioning that the new sequence ID is constructed by combining the ID of one of the input sequences, that has that same UMI, and the UMI itself.
The framework also produces a csv file with all the information of the output fastq files and extra information, that can help return from the output sequences to their corresponding input sequences. The file is named the same as the Read1 fastq file with an added _summary_table
suffix.
For more details, please refer to the wiki Running the project page.
This project is licensed under the MIT License - see the LICENSE file for details.