This is a collection of fixes for various issues I’ve had with Perl. Feel free to add any of your Perl tips here. I will move this to a wiki page if it gets too big.
All Perl scripts fail with error message “Compilation failed in require at…*.pm did not return true at …”
Unable to install packages on Debian with error message “Perl may be unconfigured”
I suspect there are probably several homemade versions of this kind of script kicking around, but here is a perl script I’ve written for turning your SNP table into a STRUCTURE input file. To use it, you should change the .txt to a .pl after downloading the script. More on STRUCTURE input files (and so much more!) is in the documentation here.
Thuy and I have made several perl scripts to trim Illumina reads, available on the zoology cluster at:
/Linux/Loren/Seq/trimIlluminaFqQual20.pl
/Linux/Loren/Seq/trimIlluminaFqQual20Phred.pl