One question about Counting number of reads per gene

[zhaofei]

Hi all,

I am using RNA STAR for getting the read count of my genes from strand specific RNASeq data.

As the manual say : column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes) ;column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

I have one gene, its count is  " 901  5  1078"

My question is why column3 (1st read strand) + column4 (2nd read strand) < column2(unstrand), why column2 ≠ column3 + column4

Thanks in advance

Fei

[Alexander Dobin]

Hi Fei,

for reads that map to genes that overlap on the opposite strands, the unstranded count will count them as ambiguous, while the stranded counting will assign them to separate genes.

Hence the unstranded count is <= sum of stranded.

Cheers

Alex