I have two questions about using masurca to assemble plant genome.
1 Do I need to reverse complement the jump library before assembling? It saids "#reverse (R2) reads are optional for PE libraries and mandatory for JUMP libraries", but it seems no flag to specify this.
2 After I execute 'assemble.sh', I got some errors:
[Sat Jun 13 16:39:50 CDT 2015] Processing pe library reads
[Sat Jun 13 16:39:54 CDT 2015] Processing sj library reads
Average PE read length 1
choosing kmer size of 31 for the graph
cat: write error: Broken pipe
[Sat Jun 13 17:44:04 CDT 2015] Creating mer database for Quorum.
[Sat Jun 13 17:53:42 CDT 2015] Error correct PE.
Cutoff computation failed. Pass it explicitly with -p switch.
Error correction of PE reads failed. Check pe.cor.log.
And there is no 'pe.cor.log' file. I don't know how to fix this. Hope somebody can help me! Thanks a lot.