Difference between revisions of "SK met"
From Crop Genomics Lab.
(Created page with "raw_data : /NGS/NGS/VignaRadiata/DNA/SK/ TBI[7]=TN1509D0657--TCCGGAGA-AGGCTATA sample[7]=SK010 TBI[57]=TN1509D0710--TAATGCGC-TAAGATTA sample[57]=SK068 TBI[177]=TN1510D0932--...") |
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− | raw_data : /NGS/NGS/VignaRadiata/DNA/SK/ | + | raw_data : /NGS/NGS/VignaRadiata/DNA/SK/ |
TBI[7]=TN1509D0657--TCCGGAGA-AGGCTATA | TBI[7]=TN1509D0657--TCCGGAGA-AGGCTATA | ||
sample[7]=SK010 | sample[7]=SK010 | ||
Line 26: | Line 26: | ||
244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함 | 244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함 | ||
− | ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa > 63 data/haggui/Vradi_ver6.fa | + | ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa > 63 data/haggui/Vradi_ver6.fa |
1. bwa index <ref.fa> | 1. bwa index <ref.fa> | ||
2. 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" | 2. 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 05:28, 23 January 2019
raw_data : /NGS/NGS/VignaRadiata/DNA/SK/
TBI[7]=TN1509D0657--TCCGGAGA-AGGCTATA sample[7]=SK010
TBI[57]=TN1509D0710--TAATGCGC-TAAGATTA sample[57]=SK068
TBI[177]=TN1510D0932--TCTCGCGC-TCAGAGCC sample[177]=SK186
TBI[43]=TN1509D0695--GAATTCGT-ACGTCCTG sample[43]=SK049
TBI[83]=TN1509D0736--TCTCGCGC-GTCAGTAC sample[83]=SK094
TBI[143]=TN1510D0898--CTGAAGCT-GCCTCTAT sample[143]=SK152
TBI[167]=TN1510D0922--TCCGCGAA-GCCTCTAT sample[167]=SK176
TBI[147]=TN1510D0902--CTGAAGCT-TAAGATTA sample[147]=SK156
244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함
ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa > 63 data/haggui/Vradi_ver6.fa
1. bwa index <ref.fa> 2. 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"