How do I convert a flow file (.FLOW) into fastq file.

Question

[m.niwano]

Hello. I am new to bioinformatics and I have a question regarding this file format (.FLOW)

I was given a dataset consist of flow files (extention with .FLOW) from 454 pyrosequencing, and I don't know how to convert this into fastq file for further analysis.

This flow file conrtains rows of decimal numbers (IJBVZW201D3DRJ 450 1.05 0.00 1.05 0.00 0.01 0.93 0.01)

This is first few lines within a flow file.

IJBVZW201D3DRJ 450 1.05 0.00 1.05 0.00 0.01 0.93 0.01 1.00 1.16 1.18 .........(continues)

Thank you

Answer 1

[h.mon]

You need more than just the flow values to be able to get a fastq file. The flow values, by themselves, just encodes the number of homopolymer runs of the called nucleotide, but they do not contain information about which nuceotide it is.

Typically, 454 output is a .sff file, a binary file containing base, base qualities, flow values, among other information.