Supported File Types


ArrayStar with QSeq





ArrayStar with QSeq are included within the Lasergene Genomics Suite. Below are the file types supported for import and export by each application.


Imported File Types


File Format File Extension(s) Variants Microarray QSeq (ChIP-Seq, CNV,
miRNA, RNA-Seq)
Attributes Annotations VCF SNP
ABI SOLiD files *.gff, *.csfasta 1
Affymetrix Annotation files *.csv, *.transcript.csv
Affymetrix Attributes files *.arr
Affymetrix CHP files2 / Normalized Signal Values *.chp      
Affymetrix MAGE-ML files3 *.xml  
Affymetrix read files (unnormalized)4 *.cel      
Agilent/Feature Extraction files5 *txt      
Applied Biosystems (ABI) files6 *.abi, *.ab1, *abd     1      
ArrayStar and QSeq projects *.dmaproj,*.astar      
BED files *.bed          
ClustalW Alignment files *.aln          
dbNSFP Gene files dbNSFP*_gene          
DNA Multi-seq files7 *.mseq          
ELAND Alignment files *.txt          
EMBL files *.embl, *txt     8      
FastA files *.fas, *.fa,*.nt, *txt          
FastQ files *.fastq     1      
File of Filenames (FOF) *.fof          
GCG files *.seq, *.gcg     8      
GenBank files *.gbk, *.gb          
Gene Ontology (GO) Annotation files *.gene_association.*; *.goa          
GenePix Results files9 *.gpr 1 1 1      
GeneQuest projects *.dad     8      
General Feature Format files *.gff          
HapMap Genotype SNP Table Text files10 *.txt        
Helicos files *.fa, *.txt     1      
Illumina Alignment files *.txt          
Illumina Bead Studios files11 N/A          
Illumina Microarray files12 *.csv, *.txt      
Illumina Sequence files *.fastq, *.fas, *txt, *.qseq.txt     1      
Lasergene DNA files *.seq     8      
Misc. comma-separated files13 *.csv    
Misc. text files14 *.txt    
Phred files *.phd          
Roche 454 files *.fna, *.fas, *.sff     1      
Roche NimbleGen Design files *.ngd        
Roche NimbleGen files15 *.call, *.calls      
Roche NimbleGen text files16 *.txt    
Roche NimbleGen files (unnormalized)17 *.pair, *.pair.txt      
SAM and BAM assembly files *.sam, *.bam          
SeqBuilder projects *.sbd, *.sbp     8      
SeqMan NGen assembly files 18 *.assembly    
SeqMan Pro SNP Table text files19 *.txt        
SeqMan Pro Variant Call Files (VCF) 20 *.vcf        
Single Configuration (SCF2/SCF3) files *.scf     1      
VCF Annotation files *.vcf      
VectorNTI files *.gb     8      

1 Reads only.
2 Supported CHP files for import include: Affymetrix GCOS files, Affymetrix GCCC (Calvin) files, "Quantification-only" CHP files that are the result of doing PLIER or RMA normalization on Affymetrix .cel files, "Whole-transcript” CHP files that contain information for whole-transcript arrays
3 To be readable in ArrayStar, the MAGE-ML *.dtd file must be present in the same folder as the Attributes file.
4 Contains un-normalized signal data from Affymetrix. In order to interpret and normalize data from .cel files, ArrayStar requires a .cdf file (for 3’ expression chip types) or a .pgf file (for whole-transcript arrays).
5 Contains data from one chip with one or two color channels.
6 ArrayStar does not support ABI files without base calls.
7  ArrayStar does not recognize features saved in *.mseq files as annotations.
8 Template only.
9 Contains data from one chip with two color channels. When importing *.gpr files, ArrayStar uses the linear values from the “Ratio of Medians” column as the signal intensity values.
10 Imported from HapMap via the Data Import Wizard.
11 See ArrayStar Help for more information.
12 Contains either gene-level data (“Group Gene Profile” or “Sample Gene Profile”) or probe-level data (“Group Probe Profile” or “Sample Probe Profile”).
13 Any user-defined, comma-delimited text files containing annotation or expression data.
14 Any user-defined text files containing annotation or expression data.
15 Contains expression data for single or multiple chips.
16 NimbleGen CALL-type files in TXT format. "NimbleGen Sample Key" is a type of Attributes file. For microarray projects, Attributes files may contain expression data for single or multiple chips.
17 An unnormalized file with probe level data.
18 Includes SNP data plus detailed feature, MID-tag, and sample name information.
19 Created by opening a SeqMan NGen *.assembly in SeqMan Pro and exporting SNP data. The resulting *.txt file contains SNP data, as well as basic MID-tag and feature information.
20 Created in SeqMan Pro, or obtained via free download from the 1100 Genomes Project and the NHLBI Exome Sequencing Project (ESP).


Exported File Types


File Format File Extension(s) Variants Microarray QSeq (ChIP-Seq, CNV,
miRNA, RNA-Seq)
Affymetrix CHP files / Normalized Signal Values *.chp
ArrayStar and QSeq projects *.dmaproj,*.astar
BED files1 *.bed
GenBank files *.gbk, *.gb     2
General Feature Format files1 *.gff
GenVision projects3 *.gnv, *.txt    
Misc. comma-separated files4 *.csv
Misc. text files4 *.txt
Roche NimbleGen files5 *.txt
Template and sequence files *.fas    
Wiggle files3 *.wig    

1 Must be selected in Configure Advanced Options before processing.
2 Template only.
3 Export is in a graph format. Must be selected in Configure Advanced Options before processing.
4 Only available in Gene Table view.
5 NimbleGen CALL-type files in TXT format.