Difference between revisions of "SK met"
From Crop Genomics Lab.
| Line 1: | Line 1: | ||
| + | == materials == | ||
raw_data : /NGS/NGS/VignaRadiata/DNA/SK/ | raw_data : /NGS/NGS/VignaRadiata/DNA/SK/ | ||
| − | + | /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.reseqKJ.sorted.bam | |
| − | + | {| cellpadding="20" cellspacing="0" border="1" | |
| − | + | |SK010 | |
| − | + | |TN1509D0657--TCCGGAGA-AGGCTATA | |
| − | + | |- | |
| − | + | |SK068 | |
| − | + | |TN1509D0710--TAATGCGC-TAAGATTA | |
| − | + | |- | |
| − | + | |SK186 | |
| − | + | |TN1510D0932--TCTCGCGC-TCAGAGCC | |
| − | + | |- | |
| − | + | |SK049 | |
| − | + | |TN1509D0695--GAATTCGT-ACGTCCTG | |
| − | + | |- | |
| − | + | |SK094 | |
| − | + | |TN1509D0736--TCTCGCGC-GTCAGTAC | |
| − | + | |- | |
| − | + | |SK152 | |
| − | + | |TN1510D0898--CTGAAGCT-GCCTCTAT | |
| − | + | |- | |
| − | + | |SK176 | |
| − | + | |TN1510D0922--TCCGCGAA-GCCTCTAT | |
| − | + | |- | |
| − | + | |SK156 | |
| − | 244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함 | + | |TN1510D0902--CTGAAGCT-TAAGATTA |
| + | |} | ||
| + | *244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함 | ||
ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa | ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa | ||
| − | 244 > 63 data/haggui/Vradi_ver6.fa | + | *244 > 63 data/haggui/Vradi_ver6.fa |
| − | + | # bwa index <ref.fa> | |
| − | + | # cat SK_met.list | parallel --gnu -j 3 "bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam" | |
Revision as of 05:44, 23 January 2019
materials
raw_data : /NGS/NGS/VignaRadiata/DNA/SK/ /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.reseqKJ.sorted.bam
| SK010 | TN1509D0657--TCCGGAGA-AGGCTATA |
| SK068 | TN1509D0710--TAATGCGC-TAAGATTA |
| SK186 | TN1510D0932--TCTCGCGC-TCAGAGCC |
| SK049 | TN1509D0695--GAATTCGT-ACGTCCTG |
| SK094 | TN1509D0736--TCTCGCGC-GTCAGTAC |
| SK152 | TN1510D0898--CTGAAGCT-GCCTCTAT |
| SK176 | TN1510D0922--TCCGCGAA-GCCTCTAT |
| SK156 | TN1510D0902--CTGAAGCT-TAAGATTA |
- 244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함
ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa
- 244 > 63 data/haggui/Vradi_ver6.fa
- bwa index <ref.fa>
- cat SK_met.list | parallel --gnu -j 3 "bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam"
