2017 Haneul Lab note
From Crop Genomics Lab.
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Minyoung_UV_QTL
parsing genotype data(Joinmap) and phenotype data to ICImapping format(bip format) using lgcombine.py(63:/data/skyts0401/Mungbean/MY_UV/) find linkage group 2 map is wrong, construct map newly
Mungbean synchronous QTL
make loc file(244:/home/skyts0401/reseq/chr/Mungbean_chr_coseq_parse_seg_dist.loc) missing > 10%, hetero > 10, depth < 3 marker is filtered while grouping them, find vr03, vr04 is combined in a group and vr05 is splited 2 groups, check it.
Mungbean pacbio assembly
moving SAM data(align reseq data on pacbio-scaffold) from NICEM server to 244 server (244:/kev8305/SK3/)
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Minyoung_UV_QTL
QTL analysis by using IciMapping
Mungbean synchronous QTL
construct genetic map (JoinMap 4.1), just using chr 3, 4 combined and chr 5 splited linkage group. ML method, Haldane algorithm
Mungbean pacbio assembly
convert SAM format to BAM format (244:/kev8305/SK3/convertbam.sh)
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Mungbean synchronous QTL
QTL analysis by using RQTL(desktop:/Users/sky/desktop/Mungbean_syn_RQTL.csv) just for checking locus
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Mungbean pacbio assembly
coping sorted.bam file from 244 server to 63 server