Redbean

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