Entering edit mode
9.1 years ago
dina.hesham139
▴
170
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?
