Configuring STARS on Bio-Linux

Troubleshooting

When assembling a plate, an error message comes up that says 'Warning, there may have been an error entering sequences'

This may be because phred does not recognise the sequencer or chemistry that's written in the headers of your trace files. Try assembling two traces manually using pregap4/gap4 (with the phred module selected) - this should give you a more informative message about what needs to be added to the phred configuration file.

For example, we use BigDye version 3 on a 3730 sequencer - this is not recognised by default and the following line had to be added to the /usr/software/phred/phred/phredpar.dat file

"DT3730POP7{BDv3}.mob"    terminator    big-dye    ABI_3700

Previous | Next