Question: Count Unique Alignments in BAM file
0
gravatar for colin.kern
2.4 years ago by
colin.kern180
United States
colin.kern180 wrote:

I want to get the number of alignments in my bam file that aren't duplicates. I've run Picard Tools to mark duplicates on the bam file, but didn't use the option to actually remove them. I'd prefer not to rerun that step, but I can't figure out how to get a count of this. The samtools flagstat output gives one number (6,689,555) for duplicates, but samtools view -c -F 1024 gives something different (3,266,467). I'm confused.

rna-seq alignment • 1.0k views
ADD COMMENTlink modified 2.4 years ago by geek_y8.8k • written 2.4 years ago by colin.kern180
0
gravatar for geek_y
2.4 years ago by
geek_y8.8k
geek_y8.8k wrote:

You should be using -f instead -F

ADD COMMENTlink written 2.4 years ago by geek_y8.8k
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