archive:bioinformatic_tools:jellyfish
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision | Next revision Both sides next revision | ||
|
archive:bioinformatic_tools:jellyfish [2011/05/16 20:37] karplus Added numbers from Illumina run 1 counts |
archive:bioinformatic_tools:jellyfish [2011/05/26 01:58] karplus [Banana Slug] Added post-SeqPrep estimates |
||
|---|---|---|---|
| Line 38: | Line 38: | ||
| Total distinct: 2,298,220,805 (19-mers) 2,699,479,169 (22-mers) | Total distinct: 2,298,220,805 (19-mers) 2,699,479,169 (22-mers) | ||
| These counts were done before running SeqPrep, so include adapter reads. | These counts were done before running SeqPrep, so include adapter reads. | ||
| + | |||
| + | After running SeqPrep, using all the illumina data produced | ||
| + | |||
| + | {{:bioinformatic_tools:fit-gamma-illumina-all-seqprep.png|}} | ||
| + | |||
| + | We have 2196163636 distinct 19-mers. If we use 2-or-less as the criterion for calling a k-mer a sequencing error, we get 1,222,498,009 distinct k-mers---close to our previous estimates. | ||
| + | |||
| + | The fit-gamma-illumina-all-seqprep.gnuplot script gives an estimated coverage of 10.247. If we divide the total number of k-mers (23731306715) by the approximate coverage, we get a genome length of 2.3159 Gbases. | ||
| + | |||
| ====== Gamma distribution is wrong ====== | ====== Gamma distribution is wrong ====== | ||
archive/bioinformatic_tools/jellyfish.txt · Last modified: 2015/07/28 06:23 by ceisenhart
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
