Question: Get # of unique mapped reads from Tophat output
3
gravatar for colin.kern
3.8 years ago by
colin.kern220
United States
colin.kern220 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 • 1.8k views
ADD COMMENTlink modified 3.8 years ago by Devon Ryan89k • written 3.8 years ago by colin.kern220
3
gravatar for Devon Ryan
3.8 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

samtools view -c -F 256 accepted_hits.bam

ADD COMMENTlink written 3.8 years ago by Devon Ryan89k
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