Difference between revisions of "Revio seq"
From Crop Genomics Lab.
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-a 옵션 넣어줘야 sam/bam | -a 옵션 넣어줘야 sam/bam | ||
| + | |||
| + | java -jar ./picard.jar AddOrReplaceReadGroups I=taegwang_hifi_re.bam O=taekwang_hifi_rg.bam RGLB=libtaekwang RGPL=pacbio RGPU=unit1 RGSM=Taekwang | ||
| + | 뒤에 GATK 할때 자꾸 에러남 (--sample-name) , sample name 미리 지정 | ||
samtools index SS2-2_hifi_re.bam | samtools index SS2-2_hifi_re.bam | ||
Revision as of 07:53, 23 May 2024
bioconda 깔았음
barsh 에 export 추가했음, path 설정안돼있으면 source ~/.barsh
minimap2 로 mapping Gmax ver2 fa indexing 한 후
minimap2 -x map-pb -t 10 -a /data/ref/Gmax/assembly/Gmax_275_v2.0.fa SS2-2.hifi_reads.fastq | samtools sort -o SS2-2_hifi_re.bam --write-index
-a 옵션 넣어줘야 sam/bam
java -jar ./picard.jar AddOrReplaceReadGroups I=taegwang_hifi_re.bam O=taekwang_hifi_rg.bam RGLB=libtaekwang RGPL=pacbio RGPU=unit1 RGSM=Taekwang
뒤에 GATK 할때 자꾸 에러남 (--sample-name) , sample name 미리 지정
samtools index SS2-2_hifi_re.bam
