Difference between revisions of "Redbean"
From Crop Genomics Lab.
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− | '''Reference ver3 | + | '''Reference ver3 193:/data2/k821209/Redbean/ver3/ref/''' |
− | annotation : /data2/k821209/Redbean/ver3/ref/adzuki.ver3.annot.txt | + | annotation : 193:/data2/k821209/Redbean/ver3/ref/adzuki.ver3.annot.txt |
− | + | NBS-LRR : 63:/data2/k821209/Redbean/Rgene | |
− | + | Orthomcl : 63:/data2/k821209/Redbean/Orthomcl/ver3/ | |
− | + | soap3 map : 63:/data2/k821209/Redbean/soap3/ver3 | |
− | + | beast : 193:/data2/k821209/Redbean/ver3/mcscanx/beast/temp/ok/ | |
− | + | Va2Vnaka : 193:/data2/k821209/Redbean/soap3/ver3/domestication/Va2Vn.bp.1e5.out7 | |
+ | Vnaka : 193:/data2/k821209/Redbean/ver0/nakashimae/maker/nakashimae.contig.maker.output/ | ||
'''mapman GO''' | '''mapman GO''' |
Latest revision as of 06:29, 14 August 2014
Reference ver3 193:/data2/k821209/Redbean/ver3/ref/
annotation : 193:/data2/k821209/Redbean/ver3/ref/adzuki.ver3.annot.txt NBS-LRR : 63:/data2/k821209/Redbean/Rgene Orthomcl : 63:/data2/k821209/Redbean/Orthomcl/ver3/ soap3 map : 63:/data2/k821209/Redbean/soap3/ver3 beast : 193:/data2/k821209/Redbean/ver3/mcscanx/beast/temp/ok/ Va2Vnaka : 193:/data2/k821209/Redbean/soap3/ver3/domestication/Va2Vn.bp.1e5.out7 Vnaka : 193:/data2/k821209/Redbean/ver0/nakashimae/maker/nakashimae.contig.maker.output/
mapman GO
193:/data2/k821209/Redbean/ver1/mapman/Va.GO.txt # based on ver1
links
http://database.prota.org/PROTAhtml/Vigna%20angularis_En.htm
GBS
- joinmap and anchoring : 193:/data2/k821209/synteny_based_scaffolding/synteny_based_scaffolding_ver1/ver1/Pv/joinmap
SNP
- snp based coding seq retrieve: 63:/data2/k821209/Redbean/SNP/ # based on ver1
Synteny based assembly
ver1 : 193:/data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/ - reference sequences : adzuki.ref.fasta - gene prediction : adzuki.ref.all.gff.maker.gff.sorted.gff3 - coding sequences : adzuki.ref.fasta.cds.fa - peptide sequences : adzuki.ref.fasta.pep.fa - interpro annotation : adzuki.ref.fasta.pep.fa.noasterix.fa.tsv - annotation parsed : /data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/adzuki.ref.fasta.pep.fa.noasterix.fa.tsv.annot
ver3 : 193:/data2/k821209/Redbean/ver3/ - reference sequences : /data2/k821209/Redbean/ver3/adzuki.ref.fa - repeat contents : /data2/k821209/Redbean/ver3/repeat/adzuki.ref.fa.out - gene contents :
Transcriptome assemblies and illumina reads
63:/data1/Sequencing/NICEM/Redbean/
MCSCANX results
193:/data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/mcscanx/ - Va2Va : V.angularis, within genome synteny - Va2Gm : V.angularis vs G.max - Va2Pv : V.angularis vs P.vulgaris - Va2Vr : V.angularis vs V.radiata
MCSCANX results - QTL
244:/home/hayasen/Workspace/Vigna/redbean/mcscanx/Va2Gm/Va2Gm.collinearity.kaks.block_r_q_pos.dic.QTL_info.txt