Entering edit mode
6.9 years ago
AAK85
•
0
Hi All I was wondering if anyone can help me with the answer of this formula:
[(number of bases in an interval * number of primary alignments)/ number of reads in an interval] *1e9
[number of bases in an interval * total number of reads)/ number of reads in an interval] * 1e9
I have the $7 and $8 column representing the starting point and ending point of an interval. I have the number of primary alignmets through this command: samtools view -F 0x100 A.bam | awk 'END {printf NR " "}' I have number of reads in an interval by this command : samtoold view -F 0X100 A.bam " chr1:10000-10468" | wc -l Now I want to know what do we get using these data in the formula and what the result of the formula represent? Thank you.