Project progress update (week3)

lortizb commented 4 years ago

Weekly progress update of my project

lortizb commented 4 years ago

Activities done:

1-I ran Canu in all my samples. It worked very well. I had 3 samples (from a total of 10) with too many short reads and Canu was not assembling these genomes; however I used the option stopOnReadQuality=false and finaly I got the draft genomes for all 10 samples.

2-I started running Nanopolish for one of the draft genome described previously. Since I have 5 contigs in this genome, I ran Nanopolish in the first contig (called tig00000002) and worked very well (I got the polished contig). However, when I ran it in the next contig (called tig00000005), I got this error: "no polishing windows found for tig00000002". Next week I will work on that.

The script can be found at: URL to the script in the GitHub issue: https://github.com/lortizb/GENE8940.git Git revision: commit 3cb81086cddb49e0cdbd01e2a897737f02e9c53b

My files are located in (Sapelo2): /scratch/lo50936/Data_analysis/Nanopore/Data_analysis/TEST2/

cbergman commented 4 years ago

14 Nov update is very good. Worked with student to identify the source of this error, but student found on her own that it was due to version of nanopolish. 2/2

lortizb / GENE8940

Project progress update (week3) #9