archive:bioinformatic_tools:quake
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archive:bioinformatic_tools:quake [2011/05/09 17:53] eyliaw [Running Quake] |
archive:bioinformatic_tools:quake [2011/05/09 18:03] eyliaw [Running Quake] |
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| correct -f [fastq file list] -k [k-mer size] -c [cutoff] -m [counts file] -p [number of cores] -z (gzips the output) | correct -f [fastq file list] -k [k-mer size] -c [cutoff] -m [counts file] -p [number of cores] -z (gzips the output) | ||
| - | In the file list, you should tab-separate paired end reads. | + | In the file list, you should tab-separate paired end reads. Also, be sure that all .'s in the sequence are written as N's. If the quality scores are written as Phred + 64, you can use -q 64 to handle it. |
| [Kevin] I think that we want to select the k-mer size manually, rather than relying on quake. Their default cutoff is very conservative, and we'll probably do better over-correcting than under-correcting. | [Kevin] I think that we want to select the k-mer size manually, rather than relying on quake. Their default cutoff is very conservative, and we'll probably do better over-correcting than under-correcting. | ||
archive/bioinformatic_tools/quake.txt · Last modified: 2015/07/28 06:26 by ceisenhart
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