I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies:
1) Long read scaffold + Velvet scaffolds
2) Long read scaffold + AbySS scaffolds
3) Long read scaffold + SOAP scaffolds
However, I do not know how to denife the parameters in the config file, it looks like this:
Dear all,
I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies:
1) Long read scaffold + Velvet scaffolds
2) Long read scaffold + AbySS scaffolds
3) Long read scaffold + SOAP scaffolds
However, I do not know how to denife the parameters in the config file, it looks like this:
I have read the manual but I still do not understand. What number I should put at mateAn_A, mateAn_B, bowtie2_maxins, bowtie2_minins, meta2fasta?
I do not know the insert size of the short reads, can someone help me with deciding he numbers in bold?
Thank you!
Kenny