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!
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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