Ngs ConvertNgsFiles.pdf
Convert NGS Data
Overview
The Convert NGS Data command allows the user to specify a set of input files, and convert these files to a set of target file formats. Source file formats include BAM, SAM, FASTQ, FASTA, and SOAP.
To access this function, click NGS | Tools | Convert Files:
Input Data Requirements
The following conversions can occur:
BAM->SAM, FASTQ, FASTA, FASTQ.GZ
SAM->BAM, FASTQ, FASTA, FASTQ.GZ
FASTQ->FASTA
FASTA->FASTQ
Target files will be generated in the same folder as source files with the specified target file extensions.
Note, when converting from BAM/SAM back to raw reads, only BAM/SAM -> FASTQ.GZ will sort read name and get one entry for each read name. FASTA or FASTQ output will keep duplicates in cases where a read mapped to more than one location.
General Options
Input
Add files to menu
- Add button will add samples by selections
- Add Folder will add all samples in the selected folder (local project only)
- Search will find files based on sample registration (server project only)
- Add list will allow users to add files from a list (even add a grouping file for alignment functions).
Options
- Source File Format - Select the appropriate format for the source files.
- Target File Format - Select the appropriate format that the the source files will be converted into.
- Job Number - Specify the number of processors to use for this task.
- Output folder - Specify the directory to output the converted files.
Output Results
When the process is complete, you should find new set of files in the specified folder.
OmicScript
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