Read Count Discrepancy
bshim181 opened this issue · comments
Hello, I am looking at read count from STAR aligner log file
Also, I have compared it to the samtools flagstat of the sorted bam file.
It seems like there is a discrepancy between two numbers and was wondering how might this happen. Thank you!
Hi Bohoon,
STAR and samtools count reads differently. There are a number of threads that discuss this.