tophat2 incomplete mapping of reads

Hey,

I was mapping a single end RNAseq fastq file (of read count 178,521,597) with tophat 2 using the following command:

tophat2 -o mapped file -p 20 -G /data2/hg19/genes.gtf /data2/hg19/genome myfile.fastq

the summary stated: Input: 566453 Mapped: 428253 (75.6% of input)

So, why the mapping was incomplete? Any clue?

rna-seq

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updated 4.0 years ago by Ram

• written 10.7 years ago by dina.hesham139

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