Bioconductor QuasR Alignment Wrapper
The add-in functions as a wrapper around the QuasR (short for Quantify and annotate short reads in R) package in BioConductor. It uses qAlign to align single or paired-end reads to a reference genome, and unmapped reads are optionally further aligned to alternative references. Pre-existing alignments in BAM format will be generated after importing.
Note: This process is a JMP Add-In and must be downloaded from the JMP File Exchange and added to your JMP Genomics installation.
What do I need?
You must download and install both the current R (version 3.0.1, or higher) package and the Bio C QuasR software application from the BioConductor website before using this process. Make note of the location of the Rterm.exe file. The location of this executable, which is required to submit R programs in batch mode, must be specified. Refer to the Instruction file under the JMP Genomics Add-Ins menu for instructions on downloading and installing these packages.
In order to import data using the Bioconductor Quas R Alignment Wrapper process, you must have a set of three types of files:
| 1 | Files containing the raw data. Raw sequence file can be compressed with gzip, bzip2 or xz (with extensions _gz, _bz, or _xz). |
| 2 | An existing JMP Genomics Experimental Design File (EDF). The EDF lists specific information about the design of the experiment. The EDF is typically a text file or Excel spread sheet, and must be created before the data can be imported. At a minimum, the EDF must contain two columns: |
| • | A column named File or FileName, whose entries identify the files containing the raw data, and |
| • | A column named SampleName whose entries correspond to the variable names in the SAS data set to be generated. |
The samples_chip_single.txt file (opened in JMP) is shown below.
| 3 | A reference genome sequence file: A reference genome is required for creating the alignment index and further alignments. |
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
Output/Results
The output data sets generated by this process are listed in a Results window. Refer to the Bioconductor QuasR Alignment Wrapper output documentation for detailed descriptions.
References
Gaidatzis D, Lerch A, Hahne F, Stadler MB. QuasR. (2015). Quantification and annotation of short reads in R. Bioinformatics 31(7):1130-1132.
Langmead B, Trapnell C, Pop M, Salzberg SL. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):R25.
Au KF, Jiang H, Lin L, Xing Y, Wong WH. (2010). Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research, 38(14):4570-8.