454 reads.fna interpretation

[litali]

Hi
I wnated to know what the values of rank, x and y, which appear in the head of each read mean. Thank you!

[kmcarr]

x and y are the x and y grid coordinates of the well on picotiter plate which produced this read. The image analysis software ranks all wells (raw reads) in order of their signal intensity. I'm not sure whether this is the average intensity of the whole read, intensity of key tag signals or some other measure. The only thing you really need to know about the rank is that the software sorts reads in rank order when it produces the .fna file. This means that the reads at the beginning of the file are the lowest intensity and the reads are the end of the file are the highest. Both of these groups of reads are likely to be the lower quality and more error prone. So if you find yourself wanting a small subset of reads to test some bit of code on and the quality of those reads matter don't just head or tail your file to get those reads.