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 | ||
| − | + | '''SNP''' | |
| + | - snp based coding seq retrieve: 63:/data2/k821209/Redbean/SNP/ | ||
'''Synteny based assembly''' | '''Synteny based assembly''' | ||
193:/data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/ | 193:/data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/ | ||
Revision as of 06:50, 24 July 2014
links
http://database.prota.org/PROTAhtml/Vigna%20angularis_En.htm
SNP
- snp based coding seq retrieve: 63:/data2/k821209/Redbean/SNP/
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
