Lets say I have chr1:65355-65398, how do i get the reads that cover this region out of the SAM? I've converted to BAM, sorted it, then indexed it, then i run it with:
samtools view align_sorted.bam chr1:65355-65398
But i return nothing, so either there''s no read in that region, or I've done something wrong along the way.
samtools view -bS align.sam > align.bam samtools sort align.bam align_sorted.bam samtools index align_sorted.bam align_sorted.bai
^^ Are the other commands I used.