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Old 11-21-2012, 05:51 AM   #1
erichpeterson
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Location: Little Rock

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Default Does accepted_hits.bam include unmapped.bam reads

Does the accepted_hits.bam file generated by Tophat2 include those placed in unmapped.bam.

I ask because when I run:
samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l

And then run:
cat sample.fq | wc -l
<result from previous command> / 4

The two values are exactly the same!
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Old 11-21-2012, 06:41 AM   #2
marcowanger
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The short answer: nope
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Old 11-21-2012, 07:08 AM   #3
erichpeterson
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Quote:
Originally Posted by marcowanger View Post
The short answer: nope
I'm interested in the long answer. It is too much of a coincidence that these numbers are the same. I'm wanting to get a percentage of mapped reads and unmapped reads of the total number of reads.

Thanks
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