Difference between revisions of "Redbean"
From Crop Genomics Lab.
| Line 11: | Line 11: | ||
- 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 | ||
'''Synteny based assembly''' | '''Synteny based assembly''' | ||
| − | 193:/data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/ | + | |
| + | ver1 : 193:/data2/k821209/Redbean/ver1/maker/adzuki.ref.maker.output/ | ||
- reference sequences : adzuki.ref.fasta | - reference sequences : adzuki.ref.fasta | ||
- gene prediction : adzuki.ref.all.gff.maker.gff.sorted.gff3 | - gene prediction : adzuki.ref.all.gff.maker.gff.sorted.gff3 | ||
| Line 18: | Line 19: | ||
- interpro annotation : adzuki.ref.fasta.pep.fa.noasterix.fa.tsv | - 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 | - 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''' | '''Transcriptome assemblies and illumina reads''' | ||
Revision as of 06:25, 25 July 2014
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
