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mapping rate from sam format

how to know the mapping rate from .sam file generated by a mapper?
do I use

samtools flagstat file.sam
Can you help me?

Thanks

mapping alignment samtools
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updated by Brice Sarver Brice Sarver • written by midox midox

1 answer

See this post: Number of mapped reads from BAM file

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updated by Ram Ram • written by Brice Sarver Brice Sarver

I haven't a paired reads. I have a long reads not paired short. How can I find the number of mapped reads or the rate? samtools flagstat is a good solution?

thanks

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updated by Ram Ram • written by midox midox

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