Examining DNA methylation using CoGe

sr320 commented 7 years ago

This week we are back to the one question quiz 🍾

This week we will be going over DNA methylation and how analyze this type of data. For this week's quiz question, each of you will use CoGe to determine DNA methylation in a single oyster sample. See table be for access to the raw data.

For this question you will need to post a url from your repo (ie md, ipynb) that fully documents your activities in a way that it can reproduced and each aspect is explained. This includes providing links to data generated, and picture of genome browser showing your data.

Then, once you find a region that is interesting (ie lots of DNA methylation)- use blast to identify a sequence in your taxa of interest that is related.

ID	file
sr320	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_1_s6_R1.fastq.gz`
yaaminiv	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_2_s6_R1.fastq.gz`
mmiddleton	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_3_s6_R1.fastq.gz`
aspanjer	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_4_s6_R1.fastq.gz`
jldimond	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_5_s6_R1.fastq.gz`
mfisher5	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_14_s6_R1.fastq.gz`
nclowell	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_15_s6_R1.fastq.gz`
laurahspencer	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_16_s6_R1.fastq.gz`
Ellior2	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_17_s6_R1.fastq.gz`
MeganEDuffy	`http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/zr1394_18_s6_R1.fastq.gz`