2017 Haneul Lab note

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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

variant calling (244:/kev8305/SK3/, 63:/data/skyts0401/Mungbean/mapping/resequencing/)

samtools mpileup -f falcon_500_sspace.final.scaffolds.fasta -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -b bam_list | bcftools call -v -m -O v > variants.vcf
samtools mpileup -f falcon_500_sspace.final.scaffolds.fasta -I -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -b bam_list | bcftools call -v -m -O v > variants_snp.vcf

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Mungbean pacbio assembly

variant calling Kyoungki Jarae #5 with pacbio falcon scaffold (63:/data/skyts0401/Mungbean/mapping/resequencing/)

bwa index falcon_500_sspace.final.scaffolds.fasta
bwa mem -t 10 falcon_500_sspace.final.scaffolds.fasta KJ-C_1.fastq.gz KJ-C_2.fastq.gz > KJ-pe_falcon_scaffold.sam

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Mungbean pacbio assembly

variant calling Kyoungki Jarae #5 with pacbio falcon scaffold (63:/data/skyts0401/Mungbean/mapping/resequencing/)

samtools view -Sb KJ-pe_falcon_scaffold.sam > KJ-pe_falcon_scaffold.bam
samtools sort KJ-pe_falcon_scaffold.bam -o KJ-pe_falcon_scaffold.sorted.bam
samtools index KJ-pe_falcon_scaffold.sorted.bam
samtools mpileup -f falcon_500_sspace.final.scaffolds.fasta -I -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u KJ-pe_falcon_scaffold.sorted.bam | bcftools call -v -m -O v > KJ_falcon_scaffold_variants_snp.vcf

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Jatropha assembly

make svg file for superscaffold - linkage group marker location (63:/home/skyts0401/svg/)

python make_chr_lg_svg.py standard_output.final.scaffolds.fasta.tr.JM_out.fa standard_output.final.scaffolds.fasta LG.total.txt.reformed standard_output.final.scaffolds.fasta.tr.JM_out.fa.log > chr_lg.svg

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Mungbean Chloroplast assembly

pairing Illumina PE read (63:/home/skyts0401/)

sudo python PE-pairing.py /data/jungminh/mungbean/PE/SunhwaN_1_cont.fq /data/jungminh/mungbean/PE/SunhwaN_2_cont.fq

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Mungbean Chloroplast assembly

(63:/data/skyts0401/Mungbean/chloroplast/)

gmap_build -D gmap_db -d v.radiata v.radiata.fasta
gmap --nosplicing -D gmap_db -n 1 -d v.radiata -f samse scaf_cp_20k.fasta -t 12 | samtools view -Sb > Vr-cp_scaf-cp-20k.bam
samtools sort Vr-cp_scaf-cp-20k.bam -o Vr-cp_scaf-cp-20k.sorted.bam
samtools index Vr-cp_scaf-cp-20k.sorted.bam

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Mungbean Chloroplast assembly

falcon - path : 63:/home/skyts0401/Falcon_RE/rere/

before run, copy fc_env folder (63:/data/skyts0401/Falcon/)

cp -r ~/FALCON_RE/rere/FALCON-integrate/fc_env YOUR_FOLDER

and configure file is on /home/skyts0401/fc_run.cfg


align canu contig_cp file to canu contig_cp assembly (63:/data/skyts0401/Mungbean/chloroplast/)

~/bowtie2-2.2.9/bowtie2-build Vr_cp_canu.contigs.for.mapping.fasta Vr_cp_canu.contigs.for.mapping.fasta
~/bowtie2-2.2.9/bowtie2 -x Vr_cp_canu.contigs.for.mapping.fasta -f canu_ctg_cp.fasta --end-to-end --very-fast -p 20 -S cp-assembly_canu-ctg.sam
samtools view -Sb cp-assembly_canu-ctg.sam > cp-assembly_canu-ctg.bam
samtools sort cp-assembly_canu-ctg.bam -o cp-assembly_canu-ctg.sorted.bam
samtools index cp-assembly_canu-ctg.sorted.bam
samtools faidx canu_ctg_cp.fasta