Process Description
SAM Input Engine
The SAM Input Engine imports a set of Sequence Alignment Map (.sam) files and combines them into three SAS data sets containing chromosome, location, and sequence identity of each sample with a reference sequence.
This process supports both paired-end and single-end reads.
Important: Before running this process, you must navigate to the C:\Program Files\SASHome\JMPGenomics\13\Genomics\ThirdPartyAnnotation\ folder and create a new folder and name it NextGen. You must then download SAMtools version 0.1.12 (for Windows) from https://sourceforge.net/projects/samtools/files/samtools/0.1.12/ and save the executable files in the newly created NextGen folder.
What do I need?
Before you can successfully import the raw data into SAS data sets that can be used for analysis in JMP Genomics, you must locate and gather several sources of information:
| • | An Experimental Design File (EDF) that indexes the individual raw data files for the experiment. The EDF is typically a text file or Excel spread sheet and must be created before the data can be imported. |
Important: The EDF used for importing SAM data must contain a variable called SampleName. The values listed in this column identify each sample in the experiment. Providing this name allows the SAM data for each sample, which are typically spread across multiple .sam files, to be merged into one SAS data set.
| • | All of the .sam files containing the raw data, which must be located and copied to a single folder. Each .sam file corresponds to an individual chromosome and contains the hybridization intensities for that array. |
The following example uses .sam files for the Y chromosome of two different mice (from the list shown below) that were downloaded from The 1000 Genomics Project and saved in the Next-Gen\SAM\GSE18905 folder created in the JMP Genomics Sample Data folder.
The EDF for this example (shown below) specifies the import of the GSM468501_MUS1_chrY.sam and GSM468501_MUS2_chrY.sam files.
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 SAM Input Engine output documentation for detailed descriptions.