Difference between revisions of "2017 Taeyoung Lab note"
From Crop Genomics Lab.
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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