SSPACE assembling Genome!
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
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Hello fufuyou!
We believe that this post does not fit the main topic of this site.
Not a real question, copy-pasted from http://seqanswers.com/forums/showthread.php?p=147022#post147022
User suspended.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
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Cheers!
Because my problem is a same problem. And this question in seqanswers is my question.
Thanks,
Fuyou