Difference between revisions of "2017 Haneul Lab note"

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(Mungbean synchronous QTL)
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=== Mungbean synchronous QTL ===
 
=== Mungbean synchronous QTL ===
 
  QTL analysis by using RQTL(desktop:/Users/sky/desktop/Mungbean_syn_RQTL.csv)
 
  QTL analysis by using RQTL(desktop:/Users/sky/desktop/Mungbean_syn_RQTL.csv)
  just for checking there is QTL
+
  just for checking locus

Revision as of 01:47, 13 January 2017

Contents

1 / 9

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/)

1 / 10

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)

1/ 11

Mungbean synchronous QTL

QTL analysis by using RQTL(desktop:/Users/sky/desktop/Mungbean_syn_RQTL.csv)
just for checking locus