Difference between revisions of "2017 Mar Taeyoung Lab note"

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(2017.3.6)
(2017.3.6)
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'''Alignment'''
 
'''Alignment'''
 
  /alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/Fafile$ python clustalw.py
 
  /alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/Fafile$ python clustalw.py
 +
 +
==2017.3.7==
 +
===BEAST analysis===
 +
'''Make xml file'''

Revision as of 04:58, 7 March 2017

Contents

2017.3.2

Venn diagram using Organ data

Flower and Endosperm data were merged

python ~/py/MakeBinaryTableForOrthomcl.py group.txt > group.txt.binary.flr.and.end
python ~/py/change_raw_and_col.py group.txt.binary.flr.and.end > group.txt.binary.flr.and.end.parsed
python ~/py/MakeRawInputUsingBinary.py group.txt.binary.flr.and.end.parsed > group.txt.binary.flr.and.end.parsed.rawfile
..

2017.3.6

OrthoMcl again with cdhit file

True Orthologous retrieving

comparing length of peptide sequences with cutoff 0.1

/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1$ python length_polyporphism.py True_orhthologous.txt > True_orhthologous.txt.length.cutoff.0.1

BEAST analysis

Make Raw File

Alignment

/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/Fafile$ python clustalw.py

2017.3.7

BEAST analysis

Make xml file