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Data Science class – Project Report

I took BIOL 419: Data Science for Biologists in Winter 2016. My project group used Jake Heare’s data from https://github.com/jheare/OluridaSurvey2014 for final project. We used various classifiers and visualization to analyze the data.

This is the link to final project report:

https://docs.google.com/document/d/1QBFr_o29CAuwWlZhbJjLeIPDhjnRwGdHzmOfN4d4b6Y/edit?usp=sharing

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Analyzing fastq files

  • Created another iPython notebook ‘BSMAP-v1′
  • Used program bsmp-2.74 to compare the files with template genome to observe the methylation pattern.

-a is query file

-d is reference sequence file (In ‘halfshell’ on OWL)

-o is output alignment file (Saved in ‘analyses’ folder in ‘Mrunmayee’ (OWL server))

  • Others used for creating methratio_out_{i}_b.txt files:

-u = report unmapped reads

-z = base quality

-g = gap size

-s = seed size

  • Also used for loop to go through files and count the number of lines to make sure that there is no glitch
  • cd.. = switches directory to one above
  • = next line
  • Useful code is in SR github: LabDocs/code/bash.md
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using IPython and command line

Trying to open and work with notebook and command line by myself turned out to be more difficult than I thought.

All the commands and code I used on Wednesday and Friday:

  • Type ‘cd <drag the directory> ipython’ to select that as a directory in command line
  • To open the notebook ‘ipython notebook’ in command line
  • Upload the screenshots to owl server to link in notebook (Make sure to rename!)
  • Couldn’t get the markdown to embed image to work. Used HTML instead -

“from IPython.display import Image

from IPython.core.display import HTML

Image(url = “<image url>”)”

  • Got markdown to work later! (Turns out I was trying to use it as code

 

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Summary of new project

Comparing the DNA methylation pattern of oysters to see if the location the oysters are planted at changes the expression of some genes.

The oysters had parents from the same the location. Half the number of oysters of F1 generation were planted at Fidalgo Bay and the other half were planted at Oyster Bay

Things I learned today:

  • how to use command line to access the iPython notebook on web.
  • how to access files on the computer from the notebook
  • how to check quality of the data

Note: Only methylated cytosine remain as cytosine after disulfide sequencing. Others are turned into Uracil.

 

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DNA Extraction 1/20/16

The four oyster DNA samples ( 2HL # 28 – 31) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees.

DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed.

Later the samples were stored in refrigerator in box ‘Oly gDNA Oly Reciprocal Transplant Final Sampling Box #2’.

 

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DNA Extraction 1/14/16

The four oyster DNA samples ( 2HL # 24 – 27) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees.

DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed.

Later the samples were stored in refrigerator in box ‘Oly gDNA Oly Reciprocal Transplant Final Sampling Box #2’.

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DNA Extraction 1/12/16

The four oyster DNA samples ( 2HL # 20 – 23) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees.

DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed.

Later the samples were stored in refrigerator in box ‘Oly gDNA Oly Reciprocal Transplant Final Sampling Box #2’.

 

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DNA Extraction 12/17/2015

The four oyster DNA samples ( 2HL # 16 – 19) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees.

DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed.

Later the samples were stored in refrigerator in box ‘Oly gDNA Oly Reciprocal Transplant Final Sampling Box #2’.

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DNA Extractions 12/11/2015

The four oyster DNA samples ( 2HL # 12 – 15) incubated at 60 degree for an hour. Samples were previously stored at -80 degrees. It didn’t seem like there was any tissue in sample #13.

DNA was extracted from them using the mollusc DNA extraction kit. None of the optional steps were performed.

Later the samples were stored in refrigerator in box ‘Oly gDNA Oly Reciprocal Transplant Final Sampling Box #2’.

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