To import data into a Partek^® Flow^® project, first transfer the files to the server. This is done using the button prior to file type selection or by using the  transfer files link after the file type has been selected. 

Partek^® Flow^® can import a wide variety of data types including raw counts, matrices, microarray, variant call files as well as unaligned and aligned NGS data.

The following file types are valid and will be recognized by the Partek Flow file browser. Seurat Rds files or CEL and Idat microarray files should be unzipped before transfer to the server, otherwise there is no need to unzip compressed files.:   

In cases where paired end fastq data is present, files will also be automatically recognized and their paired relationship will be maintained throughout the analysis.

Matching on paired end files is based on file names: every character in both file names must match, except for the section that determines whether a file is the first or the second file. For instance, if the first file contains "_R1", "_1", "_F3", "_F5" in the file name, the second file must contain something in the lines with the following: "_R2", "_2", "_F5", "_F5-P2", "_F5-BC", "_R3", "_R5" etc. The identifying section must be separated from the rest of the filename with underscores or dots. If two conflicting identifiers are present then the file is treated as single end. For example, s_1_1 matches s_1_2, as described above. However, s_2_1 does not mate with s_1_2 and the files will be treated as two single-end files.

Apart from paired-end data, files with conventional filename suffixes that indicate that they belong to the same sample are consolidated. These suffixes include: 

• Adapter sequences
  • "_bbbbbb" followed by "_" or at the end of the file name, where each "b" is "A", "C", "G", or "T"
• Lane numbers
  • "_L###" followed by "_" or at the end of the file name, where each "#" is a digit 0 to 9

• Dates

  • in the form "####-##-##" preceded or followed by a period or underscore

• Set number 

  • of the form "_###" from the end

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