Difference between revisions of "Redbean"
From Crop Genomics Lab.
| Line 1: | Line 1: | ||
'''links''' | '''links''' | ||
http://database.prota.org/PROTAhtml/Vigna%20angularis_En.htm | 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''' | ||
- snp based coding seq retrieve: 63:/data2/k821209/Redbean/SNP/ # based on ver1 | - snp based coding seq retrieve: 63:/data2/k821209/Redbean/SNP/ # based on ver1 | ||
Revision as of 07:52, 24 July 2014
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
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
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
