Question: Get # of unique mapped reads from Tophat output
3
gravatar for colin.kern
4.6 years ago by
colin.kern770
United States
colin.kern770 wrote:

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 • 2.1k views
ADD COMMENTlink modified 4.6 years ago by Devon Ryan93k • written 4.6 years ago by colin.kern770
3
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

samtools view -c -F 256 accepted_hits.bam

ADD COMMENTlink written 4.6 years ago by Devon Ryan93k
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