2017 Mar Taeyoung Lab note

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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


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


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


BEAST analysis

Make xml file


Organ transcriptome cdhited OrthoMcl


/alima9002/63_backup/Jatropha/OrthoMCL/Organ_cdhit$ blastp -db goodProteins.fasta -query goodProteins.fasta -outfmt 6 -out goodProteins.fasta.allvall -num_threads 8 -evalue 1e-5 -seg yes -soft_masking true -max_target_seqs 999999999

BEAST using no length polyporphism loci

Prottest for select best substitution model

/data2/alima90/Jatropha/same_length_BEAST/$ python prottest.py

retrieve only JTT

/data2/alima90/Jatropha/same_length_BEAST/JTT$ python ret_JTT_only.py 

Make xml template using beauti

JTT/length of chain : 50 million

Make xml

/data2/alima90/Jatropha/same_length_BEAST/JTT$ python beast.xml.parsing.py Jct_10060_c0_g1_i1.xml

Running BEAST

/data2/alima90/Jatropha/same_length_BEAST/JTT$ python run_beast.py

KaKs to filter more loci in BEAST analysis

Jat species cdhited blast na1 again

/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1$ python blastp.py