Difference between revisions of "2017 Mar Taeyoung Lab note"

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(2017.3.15)
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===get fasta file===
 
===get fasta file===
 
  python get_fasta.py gene.fpkm.fc2.txt.2overlap.list.S7 > gene.fpkm.fc2.txt.2overlap.list.S7.fa
 
  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
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===make a tree===
 +
/alima9002/program/PhyML-3.1/PhyML-3.1_linux64 -i all.seq.fa.i.phylip -d aa -b 500 -m JTT

Revision as of 08:34, 22 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