MiSeq Reporter Specifications


Secondary Analysis Input Requirements

The MiSeq Reporter requires the following primary analysis files to begin secondary analysis. The software automatically accesses these files in the run folder.

File Type Description
RTAComplete.txt Marker file that indicates that RTA processing is complete.
SampleSheet.csv Provided at the beginning of a sequencing run. Contains analysis workflow and important run information.
RunInfo.xml Identifies high-level run information.
*.bcl files Files contain base calling information.
*.filter files Files contain filter results for each tile.
*.locs files Files contain the locations of all clusters on a tile.

Pre-Installed Databases and Genomes


miRbase for human

dbSNP for human

refGene for human

Genomes Arabidopsis thaliana


E. coli strain DH10b

human (Homo sapiens) build hg19




Staphylococcus aureus

You can upload and use your own reference in FASTA format. Reference FASTA files should be stored in a single folder and have a *.fa or *.fasta extension.