Input Specifications

ATOPlex accepts the following inputs:

CSV File / BED file

• Genomic Regions

  Genomic regions required fields are chrom, start, end and name, the format need to use tab-delimited.
  Bed or csv file is also supported and can be upload as input.

  Note: In ATOPlex system, genomic regions are represented as number pairs (start base, end base) using the Reference Genome. The genomic coordinates inputs follows the convention “1-based start, 1-based end“, for example, the chromosome 1 first 100 bases are defined as chrom=chr1, start=1, end=100, name=test . If your target region is about dbSNP position, you can set the chromStart=chromEnd, for example, the rs10411210 snp is defined as chrom=chr19,start=33532299, end=33532299, name=rs10411210.

  genomic regions formats as follow:
  chr1 45965995 45966095 MMACHC001
  chr1 100671776 100671867 DBT004
  chr19 33532299 33532299 rs10411210

  Download bed file example
  Download csv file example

• Gene List
  A gene list is a text file of list containing Gene Symbols with only one column, while 'CDS' or 'Exon' is need simultaneously.

  gene list formats as follow：
  BRIP1
  BARD1
  CDK12

  Download text file example

  Notes
  ATOPlex would not work if the length of target regions is over 400kbp or target counts over 2000. You can contact with us to require customized assistance (MGI_ATOPlex@mgi-tech.com).