archive:bioinformatic_tools:quake
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archive:bioinformatic_tools:quake [2011/05/09 18:04] eyliaw [Running Quake] |
archive:bioinformatic_tools:quake [2011/05/27 21:12] eyliaw |
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| They also recommend a kmer probability of 0.01 in a random sequence that is as long as the genome. That is, 2*G/4^k ~ 0.01, where G is the size of the sequenced genome and k is the size of the kmer. Simplified, k ~ log4(200*G), which is about 19 for our prediction of the banana slug genome size, {{https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish|2.042e+09}}. | They also recommend a kmer probability of 0.01 in a random sequence that is as long as the genome. That is, 2*G/4^k ~ 0.01, where G is the size of the sequenced genome and k is the size of the kmer. Simplified, k ~ log4(200*G), which is about 19 for our prediction of the banana slug genome size, {{https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish|2.042e+09}}. | ||
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| + | ===== Potential Problems ====== | ||
| + | * Input files need to have an extension, or Quake will throw a substr error when trying to merge hidden files into a result. | ||
| + | * With paired-end input, Quake will output two files for each paired-end read. One will be the cor.fastq file, which contains corrected, paired reads. The other will be the cor_single.fastq file, which contains reads where only one pair could be corrected. You can treat the cor_single.fastq file as a single read file. | ||
archive/bioinformatic_tools/quake.txt · Last modified: 2015/07/28 06:26 by ceisenhart
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