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Hi all,
I have two .fastq files of Illumina pair-end data (reads1.fastq & reads1.fastq).
All files together have 28803268 reads.
The output of Tophat2 are accepted_hits.bam and unmappted.bam.
Counting mapped and unmapped reads gives 34968712 reads.
samtools view -c -F 4 accepted_hits.bam # = 25839522
samtools view -c -f 4 unmapped.bam # = 9129190
25839522 + 9129190 = 34968712
34968712 != 28803268
Can you explain me why Tophat2 outputs more reads than are in input?
I have two .fastq files of Illumina pair-end data (reads1.fastq & reads1.fastq).
All files together have 28803268 reads.
The output of Tophat2 are accepted_hits.bam and unmappted.bam.
Counting mapped and unmapped reads gives 34968712 reads.
samtools view -c -F 4 accepted_hits.bam # = 25839522
samtools view -c -f 4 unmapped.bam # = 9129190
25839522 + 9129190 = 34968712
34968712 != 28803268
Can you explain me why Tophat2 outputs more reads than are in input?
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