depth_and_breadth_of_coverage
Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revision | |||
| depth_and_breadth_of_coverage [2025/08/08 16:54] – 134.190.145.228 | depth_and_breadth_of_coverage [2025/08/08 17:18] (current) – 134.190.145.228 | ||
|---|---|---|---|
| Line 51: | Line 51: | ||
| conda deactivate | conda deactivate | ||
| - | # convert to bam | + | # indexing |
| for BAM in *.bam; do | for BAM in *.bam; do | ||
| samtools index -@ 40 $BAM $BAM.bai | samtools index -@ 40 $BAM $BAM.bai | ||
| Line 90: | Line 90: | ||
| < | < | ||
| ## then align paired reads | ## then align paired reads | ||
| - | bwa-mem2 mem -t 40 ${ASSEMBLY%.fasta} $R1 $R2 | samtools view -b -F 256 | samtools sort --threads 40 -o ${PREFIX}-pe.sort.bam - | + | bwa-mem2 mem -t 40 ${ASSEMBLY%.fasta} $R1 $R2 | samtools view -b -H -F 256 | samtools sort --threads 40 -o ${PREFIX}-pe.sort.bam - |
| </ | </ | ||
| Line 98: | Line 98: | ||
| < | < | ||
| - | samtools view -b -F 256 <BAM> > < | + | samtools view -b -H -F 256 <BAM> > < |
| </ | </ | ||
depth_and_breadth_of_coverage.1754682842.txt.gz · Last modified: by 134.190.145.228