Question: Count Unique Alignments in BAM file
0
gravatar for colin.kern
22 months ago by
colin.kern150
United States
colin.kern150 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 • 794 views
ADD COMMENTlink modified 22 months ago by geek_y8.6k • written 22 months ago by colin.kern150
0
gravatar for geek_y
22 months ago by
geek_y8.6k
geek_y8.6k wrote:

You should be using -f instead -F

ADD COMMENTlink written 22 months ago by geek_y8.6k
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