Question: Why # Of Reads From Accepted_Hits.Bam + Unmapped.Bam > # Of Reads In Fastq File?
2
gravatar for newDNASeqer
6.5 years ago by
newDNASeqer670
United States
newDNASeqer670 wrote:

a quick question:

After running Tophat with a fastQ files, I found the # of reads from (accepted_hits.bam and unmapped.bam) is greater than the # of reads in fastQ file. Why is this? I thought the accepted_hits.bam plus unmapped should add up to the total # of reads that tophat started with.

I use samtools view -c to count the total reads in both accepted_hits.bam and unmapped.bam, and used grep "^@" to count the # of reads in fastQ file.

reads tophat fastq • 2.4k views
ADD COMMENTlink modified 6.5 years ago by S_Z30 • written 6.5 years ago by newDNASeqer670
3
gravatar for S_Z
6.5 years ago by
S_Z30
Germany
S_Z30 wrote:

checking following setting of tophat: -g/--max-multihits

ADD COMMENTlink written 6.5 years ago by S_Z30

Basically, the number of entries in the bam is not the number of READS, but the number of ALIGNMENTS. And if there are multiple alignments allowed per read, you will have more alignments than reads.

ADD REPLYlink written 6.5 years ago by Madelaine Gogol5.1k
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