Grace’s Notebook: National Doughnut Day

Today I helped reformat references for Mac’s paper. Will revisit a little later because I was unable to use paper pile – had to do it manually – and want to triple-check for any mistakes.

I am also continuing with Rhonda’s oyster seed morphology measurements. I took pictures of the next several tubes so I have the images on my computer to work on. The link to the oyster seed measurement is: Here. The new measurements are under the tab labeled “Cryotubes” with ongoing summary statistics in the blue cells. The link to the cryotube images is: Here.


Oly Assembly try 2: It’s yuuuuuuge!

So after hearing from Katherine about some ideas for using Platanus, I tried running the Illumina assembly once more, this time using a kmer length of 20. This seems to have had an effect, as the output contig file went from 21mb in size, to 1.9gb. I’m shuffling files around and haven’t had a chance to actually look at the contents of the file, but I’m at least heartened by the massive size increase. Size = data, right?

Assembly-stats output:

D-69-91-148-111:RobertsLab Sean$ ~/Documents/RobertsLab/assembly-stats/build/assembly-stats ~/Documents/RobertsLab/Oly_Out_Contig.fa 
stats for /Users/Sean/Documents/RobertsLab/Oly_Out_Contig.fa
sum = 1633553496, n = 12395459, ave = 131.79, largest = 23341
N50 = 141, n = 2124062
N60 = 115, n = 3463771
N70 = 92, n = 5003872
N80 = 69, n = 7087338
N90 = 61, n = 9624083
N100 = 58, n = 12395459
N_count = 0
Gaps = 0