archive:bioinformatic_tools:quake
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archive:bioinformatic_tools:quake [2011/05/07 11:53] eyliaw |
archive:bioinformatic_tools:quake [2011/05/09 18:03] eyliaw [Running Quake] |
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| Finally, correct the reads: | Finally, correct the reads: | ||
| - | correct -f [fastq list file] -k [k-mer size] -c [cutoff] -m [counts file] -p [number of cores] | + | correct -f [fastq file list] -k [k-mer size] -c [cutoff] -m [counts file] -p [number of cores] -z (gzips the output) |
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| + | 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. | ||
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| - | ---- | + | K-mer counts can be pre-filtered to save space |
| - | Can the k-mer counts be pre-filtered to save space? | + | |
| - | Well sort of. Once you've decided on a cutoff, Quake ignores all of the k-mers below that cutoff. So sure, you can filter the file to save some disk space. But having all of the k-mer counts is best for choosing the cutoff. My cov_model.py script to automatically choose the cutoff requires them. | + | Quake dev: |
| - | ---- | + | Once you've decided on a cutoff, Quake ignores all of the k-mers below that cutoff. So sure, you can filter the file to save some disk space. But having all of the k-mer counts is best for choosing the cutoff. My cov_model.py script to automatically choose the cutoff requires them. |
| ===== Methods ===== | ===== Methods ===== | ||
archive/bioinformatic_tools/quake.txt · Last modified: 2015/07/28 06:26 by ceisenhart
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