FASTX-toolkit in iMAC

Question

[Arash]

Hi, When I want to use FASTX-toolkit on iMAC , I get the following error "Invalid quality Score value (char '#' ord 35 quality value -29) on line 4 "

what does mean? Thank you!

Answer 1

[Michael]

I think this means that the encoding of the quality values in the fastq file is different from what the fastx tool expects. Presence of # indicates 'Sanger' encoding (Ascii code - 33):

perl -e 'print ord("#") - 33, "\n"'
2

See : http://seqanswers.com/forums/showthread.php?t=7596 for a solution.