Hello,

i have been trying to find out differential expression of gene using
different R packages. I have rice illumina sequencing data (pair end) with
100 bp. i mapped the data n rice genome using tophat now i got
accepted_hit. bam file in which details of mapping is available.

Now i am confused because it can be possible that a single read can align
on multiple position. When we count the reads for differential analysis
then same read is present in two different genes. So i have a question that
is correct or not? and i am reading genomic features R package for counting
the reads in libraries. Can anyone explain the summarizeOverlaps function?
i read manual but what is basic function of it.


Thanking you


regards
deepika

	[[alternative HTML version deleted]]

