Entering edit mode
8.4 years ago
fufuyou
▴
110
I now have another problem with the ExtendOrFormatContigs.pl script. Attempts to use bowtie failed due to problems with the output of the aligner and so I tried bwa as the aligner. However now after alignement I get this error call from the ExtendOrFormatContigs.pl script.
Bwa error; 0 at ExtendOrFormatContigs.pl line 288.
This is the line
system("$aligninput") == 0 || die "\nBwa error; $?" if($aligninput ne "");
Not sure what this means. My alignment folder looks fine. I'm trying again without the extend contigs option but I sure would like to extend my contigs before scaffolding.
Fuyou
