archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/19 17:40] jstjohn |
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| - | Note that this run combines both the illumina runs and the 454 data for banana slug. I am also experimenting with a k=35 since galt had better luck with a kmer size of 31 using SOAPdenovo than a kmer size of 23, perhaps the trend continues into larger kmers. If this doesn't work for whatever reason, I will also try shorter and longer kmers. | + | Note that this run combines both the illumina runs and the 454 data for banana slug. I am also experimenting with a k=35 since Galt had better luck with a kmer size of 31 using SOAPdenovo than a kmer size of 23, perhaps the trend continues into larger kmers. If this doesn't work for whatever reason, I will also try shorter and longer kmers. |
| We combined all fastq files into two large files representing the two read pairs. Each of these files is approximately 50GB and contain roughly 20GB of reads. Even on kolossus I am getting some out of disk space errors in the following step: | We combined all fastq files into two large files representing the two read pairs. Each of these files is approximately 50GB and contain roughly 20GB of reads. Even on kolossus I am getting some out of disk space errors in the following step: | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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