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Old 12-18-2013, 01:51 AM   #1
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default tophat2 reads count

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?
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Old 12-18-2013, 02:19 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Multiple mappings, fusion mapping (if you enabled that), etc...
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