I'm working on learning more about velvet's flags, using Illumina's DH10B paired end data.
After running it through the velvet workflow and then using mummerplot to compare it to NC_010473 (from ftp://ftp.ncbi.nlm.nih.gov/genomes/B.../NC_010473.fna), I get poor alignment.
After pushing through velvetg, I get:
Final graph has 96 nodes and n50 of 107680, max 326350, total 4459289, using 12781988/14405136 reads
But conversely, my mummerplot is kind of strange. I was wondering if anybody else had recapitulated the ILM data for themselves so I could compare my mummerplot data to it.
After running it through the velvet workflow and then using mummerplot to compare it to NC_010473 (from ftp://ftp.ncbi.nlm.nih.gov/genomes/B.../NC_010473.fna), I get poor alignment.
velveth EC_MiSeq 89 -create_binary -shortPaired -fastq -separate MiSeq_Ecoli_DH10B_110721_PF_R1.fastq MiSeq_Ecoli_DH10B_110721_PF_R2.fastq
Final graph has 96 nodes and n50 of 107680, max 326350, total 4459289, using 12781988/14405136 reads
But conversely, my mummerplot is kind of strange. I was wondering if anybody else had recapitulated the ILM data for themselves so I could compare my mummerplot data to it.
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