How can I extract sequence from a SAM file, with coordinates
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.
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The command looks correct. The file probably does not contain the region. Just do a positive control:
Then enter the chr and coords from the first entry and check if it is returned sucessfully.
and check it's 'chr1' and not just '1'