Difference between revisions of "2017 Mar Taeyoung Lab note"
From Crop Genomics Lab.
(→2017.3.6) |
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comparing length of peptide sequences with cutoff 0.1 | 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 | /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 | ||
| + | |||
| + | ==2017.3.14== | ||
| + | ===Phylip alignment=== | ||
| + | clustalw -ITERATION=ALIGNMENT -INFILE=%s -ALIGN -TYPE=PROTEIN -OUTPUT=PHYLIP -OUTFILE=%s.phylip | ||
| + | |||
| + | ===Phyml=== | ||
| + | /alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i %s -d aa -b 500 -m JTT | ||
| + | |||
| + | ==2017.3.15== | ||
| + | ===Get DEG of specific combination=== | ||
| + | python get_deg.py genes.fpkm.parsed.log2fc CS41/LS41 2 | grep fit > CS4.LS4.fpkm.fc2.txt | ||
| + | |||
| + | ===Get overlap among three combination=== | ||
| + | python get_overlap.py > gene.fpkm.fc2.txt.2overlap.list.S4 | ||
| + | |||
| + | ===Get fpkm from list === | ||
| + | python get_fpkm_from_list.py genes.fpkm.parsed.log2fc gene.fpkm.fc2.txt.2overlap.list.S4 > gene.fpkm.fc2.txt.2overlap.list.S4.fpkm.txt | ||
| + | |||
| + | ===Add annotation=== | ||
| + | python get_annotation.py gene.fpkm.fc2.txt.2overlap.list.S7.fpkm.txt > gene.fpkm.fc2.txt.2overlap.list.S7.fpkm.txt.add_ann | ||
| + | |||
| + | ===get fasta file=== | ||
| + | python get_fasta.py gene.fpkm.fc2.txt.2overlap.list.S7 > gene.fpkm.fc2.txt.2overlap.list.S7.fa | ||
| + | |||
| + | ==2017.03.22== | ||
| + | ===concatenate sequence=== | ||
| + | /alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/same_length_fasta/JTT$ python cat_seq.py | ||
| + | ===Alignment using muscle=== | ||
| + | /alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/same_length_fasta/JTT$ /alima9002/program/muscle3.8.31_i86linux64 -in all.seq.fa -phyiout all.seq.fa.i.phylip | ||
| + | ===make a tree=== | ||
| + | /alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i all.seq.fa.i.phylip -d aa -b 500 -m JTT | ||
| + | |||
| + | ==2017.03.23== | ||
| + | ===Tree check=== | ||
| + | all.seq.fa.i.phylip_phyml_boot_trees.txt is vizualized using itol | ||
| + | |||
| + | ==2017.03.28== | ||
| + | ===AMORE RNAseq again=== | ||
| + | ====calc log2fc with fpkm threshold==== | ||
| + | python parsing_gene_exp.diff.py gene_exp.diff gene_exp.diff.pair > gene_exp.diff.log2fc.m10 | ||
| + | |||
| + | ====get specific pair in whole gene set==== | ||
| + | python get_deg_from_gene_exp_diff.py gene_exp.diff.log2fc.m10 WS41/LS41 2 | grep fit | grep -v '-' > gene_exp.diff.log2fc.m10.WS4.LS4 | ||
Latest revision as of 07:54, 28 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
2017.3.14
Phylip alignment
clustalw -ITERATION=ALIGNMENT -INFILE=%s -ALIGN -TYPE=PROTEIN -OUTPUT=PHYLIP -OUTFILE=%s.phylip
Phyml
/alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i %s -d aa -b 500 -m JTT
2017.3.15
Get DEG of specific combination
python get_deg.py genes.fpkm.parsed.log2fc CS41/LS41 2 | grep fit > CS4.LS4.fpkm.fc2.txt
Get overlap among three combination
python get_overlap.py > gene.fpkm.fc2.txt.2overlap.list.S4
Get fpkm from list
python get_fpkm_from_list.py genes.fpkm.parsed.log2fc gene.fpkm.fc2.txt.2overlap.list.S4 > gene.fpkm.fc2.txt.2overlap.list.S4.fpkm.txt
Add annotation
python get_annotation.py gene.fpkm.fc2.txt.2overlap.list.S7.fpkm.txt > gene.fpkm.fc2.txt.2overlap.list.S7.fpkm.txt.add_ann
get fasta file
python get_fasta.py gene.fpkm.fc2.txt.2overlap.list.S7 > gene.fpkm.fc2.txt.2overlap.list.S7.fa
2017.03.22
concatenate sequence
/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/same_length_fasta/JTT$ python cat_seq.py
Alignment using muscle
/alima9002/63_backup/Jatropha/CDS/cdhit_blast_na1/same_length_fasta/JTT$ /alima9002/program/muscle3.8.31_i86linux64 -in all.seq.fa -phyiout all.seq.fa.i.phylip
make a tree
/alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i all.seq.fa.i.phylip -d aa -b 500 -m JTT
2017.03.23
Tree check
all.seq.fa.i.phylip_phyml_boot_trees.txt is vizualized using itol
2017.03.28
AMORE RNAseq again
calc log2fc with fpkm threshold
python parsing_gene_exp.diff.py gene_exp.diff gene_exp.diff.pair > gene_exp.diff.log2fc.m10
get specific pair in whole gene set
python get_deg_from_gene_exp_diff.py gene_exp.diff.log2fc.m10 WS41/LS41 2 | grep fit | grep -v '-' > gene_exp.diff.log2fc.m10.WS4.LS4
