Difference between revisions of "2017 Mar Taeyoung Lab note"
From Crop Genomics Lab.
(→2017.3.7) |
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==2017.3.8== | ==2017.3.8== | ||
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===Organ transcriptome cdhited OrthoMcl=== | ===Organ transcriptome cdhited OrthoMcl=== | ||
'''BLAST''' | '''BLAST''' | ||
/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 | /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 | ||
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===BEAST using no length polyporphism loci=== | ===BEAST using no length polyporphism loci=== | ||
====Prottest for select best substitution model==== | ====Prottest for select best substitution model==== | ||
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====Make xml==== | ====Make xml==== | ||
/data2/alima90/Jatropha/same_length_BEAST/JTT$ python beast.xml.parsing.py Jct_10060_c0_g1_i1.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 |
Revision as of 04:44, 8 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
2017.3.8
Organ transcriptome cdhited OrthoMcl
BLAST
/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