Difference between revisions of "HISAT2 pipeline"
From Crop Genomics Lab.
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| + | samtools sort TG_Ck_1_hisat.bam -o TG_Ck_1_hisat.sort.bam | ||
Revision as of 06:54, 14 September 2020
mapping
/data1/program/hisat2/hisat2-2.2.1/hisat2 -q --phred33 -x /data1/ref/Gmax_275_v2.0.fa.hisat --summary-file SS2-2_1_hisat_summary -p 6 -1 {forward_input.fq.gz} -2 {reverse_input.fq.gz} | samtools view -bS -q30 > {output}.bam
sort/markdup
samtools sort TG_Ck_1_hisat.bam -o TG_Ck_1_hisat.sort.bam
