Category Archives: SR lab notebook

SR lab notebook

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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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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DNA Extractions 12/9/2015

The four oyster DNA samples ( 2HL # 8 – 11) 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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