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alexdobin / STAR

RNA-seq aligner
MIT License
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Read Count Discrepancy #2109

Open bshim181 opened 2 months ago

bshim181 commented 2 months ago

Hello, I am looking at read count from STAR aligner log file

Screenshot 2024-04-04 at 3 30 18 PM

Also, I have compared it to the samtools flagstat of the sorted bam file.

Screenshot 2024-04-04 at 3 20 12 PM

It seems like there is a discrepancy between two numbers and was wondering how might this happen. Thank you!

alexdobin commented 2 months ago

Hi Bohoon,

STAR and samtools count reads differently. There are a number of threads that discuss this.