Difference between revisions of "2017 Taeyoung Lab note"

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=== Ongoing ===
 
=== Ongoing ===
 
==== Jatropha transcriptome Trinity assemble ====
 
==== Jatropha transcriptome Trinity assemble ====
 +
raw data : 244:/NGS/NGS/JatrophaCurcas/RNA
 +
Jatropha species transcriptome assemble : Jct,Jcu, Jin, Jgo, Jci, Jpo, Jmu, Jma, Jac, Rco (listed in 244:/NGS/NGS/JatrophaCurcas/RNA/list). All done
 +
Jatropha organ transcriptome assemble : Leaf, Root, Stem, Female flower, Male flower, LG, SG, Y, B. All done
  
 
==== Cdhit ====
 
==== Cdhit ====
 
  193:/data2/alima90/program/cdhit/cd-hit -i Y.cds.fa -M 10000 -o Y.cds.fa.cdhit -T 5
 
  193:/data2/alima90/program/cdhit/cd-hit -i Y.cds.fa -M 10000 -o Y.cds.fa.cdhit -T 5
 
+
193:/data2/alima90/program/cdhit/cd-hit -i LG.cds.fa -M 10000 -o LG.cds.fa.cdhit -T 5
  
 
==== UV GBS mapping (w/ joinmap) ====
 
==== UV GBS mapping (w/ joinmap) ====

Revision as of 04:45, 2 January 2017

Contents

2017 1.2

Ongoing

Jatropha transcriptome Trinity assemble

raw data : 244:/NGS/NGS/JatrophaCurcas/RNA
Jatropha species transcriptome assemble : Jct,Jcu, Jin, Jgo, Jci, Jpo, Jmu, Jma, Jac, Rco (listed in 244:/NGS/NGS/JatrophaCurcas/RNA/list). All done
Jatropha organ transcriptome assemble : Leaf, Root, Stem, Female flower, Male flower, LG, SG, Y, B. All done

Cdhit

193:/data2/alima90/program/cdhit/cd-hit -i Y.cds.fa -M 10000 -o Y.cds.fa.cdhit -T 5
193:/data2/alima90/program/cdhit/cd-hit -i LG.cds.fa -M 10000 -o LG.cds.fa.cdhit -T 5

UV GBS mapping (w/ joinmap)

KaKs calculation using scripts provided by MCscanX

244 :python /alima9002/63_backup/Jatropha/CDS/run.kaks.py