Ngs ConvertNgsFiles.pdf

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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:

TwoStep ConvertNgsFiles Menu.png

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

NGSConvertFiles1.png

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

ConvertNgsFiles

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