Hello,
When I generated a Roadmaps and a Sequences by velveth, and applied multiple times of velvetg on them, I found the results were not consistent. The resulted node number, n50 length, max length, total length, and used reads would always be greatly different each rime I ran velvetg.
I am sure I used the same Roadmaps and Sequences files for each velvetg run, and I deleted LastGraph, stats.txt, contigs.fa, Graph2, and PreGraph files but only kept Roadmaps and Sequences files before I ran velvetg.
I always used the same velvetg command line as the following,
./velvetg results -exp_cov 8 -cov_cutoff 4
But I always saw different results showing up after the assembly: e.g., n50 length varies from 300k to 500k.
More details:
- The velvet version is 1.1.04;
- My system is ubuntu 11.04;
- I used the MP (shortjump) data as described in http://gage.cbcb.umd.edu/data/Staphy...aureus/README;
- I used reverse complement reads and shuffled them into a single file.
- I used "./velveth results 23 -fastq -shortPaired data/shortjump_shuffled.fastq" to generate Roadmaps and Sequences files.
- I used "./velvetg results -exp_cov 8 -cov_cutoff 4" for assembly.
Would anyone give me some hints that what was going on? Thanks a lot!
Best,
Jeff
When I generated a Roadmaps and a Sequences by velveth, and applied multiple times of velvetg on them, I found the results were not consistent. The resulted node number, n50 length, max length, total length, and used reads would always be greatly different each rime I ran velvetg.
I am sure I used the same Roadmaps and Sequences files for each velvetg run, and I deleted LastGraph, stats.txt, contigs.fa, Graph2, and PreGraph files but only kept Roadmaps and Sequences files before I ran velvetg.
I always used the same velvetg command line as the following,
./velvetg results -exp_cov 8 -cov_cutoff 4
But I always saw different results showing up after the assembly: e.g., n50 length varies from 300k to 500k.
More details:
- The velvet version is 1.1.04;
- My system is ubuntu 11.04;
- I used the MP (shortjump) data as described in http://gage.cbcb.umd.edu/data/Staphy...aureus/README;
- I used reverse complement reads and shuffled them into a single file.
- I used "./velveth results 23 -fastq -shortPaired data/shortjump_shuffled.fastq" to generate Roadmaps and Sequences files.
- I used "./velvetg results -exp_cov 8 -cov_cutoff 4" for assembly.
Would anyone give me some hints that what was going on? Thanks a lot!
Best,
Jeff
Comment