Hi,

I used RSEM for transcriptome analysis to know the expression of the genes. It gave me value of read count say for one gene (G1) its 1330. RSEM also generates bam file. Using this BAM I generated the sorted bam and its bai file using samtools to view in IGV. But while visualizing in IGV It was showing large number of reads mapping to the gene G1 say 2700. What would be the reason for this? Should I stick to the values shown by RSEM or do I need to do something else so as IGV display exact read count as that of RSEM.