Get # of unique mapped reads from Tophat output · Biostar

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Get # of unique mapped reads from Tophat output

I'm using Tophat to align RNA-Seq reads to a genome. I want to know how many reads aligned, but I didn't know about the -g option when I ran Tophat, so the normal commands like "samtools -c accepted_hits.bam" isn't giving me the number of unique reads in the file, it's giving me the total number of alignments. Is there any way I can get this information without re-running Tophat?

rna-seq tophat

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updated 11.1 years ago by Devon Ryan

• written 11.1 years ago by colin.kern

1 answer

samtools view -c -F 256 accepted_hits.bam

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written 11.1 years ago by Devon Ryan

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