Hi All,

I am analyzing RNAseq data for 12 samples with and without treatment performed on  Hiseq illumina platform ( paired end ,100 bp reads, 40 million reads / sample) quality of fastaq files is fine. At this step, I am interested in DGE rather than splicing data.

I used Bowtie integrated in QuasR package for mapping the RNAseq data to reference genome (GRCh38).

The % of reads mapped to reference genome is about 50% in all files, is this % ok to perform DGE 

Thanks

Actually, QuasR uses the Bioconductor packages RBowtie and SpliceMap to map segments of the reads allowing for gaps. 50% is too low. However, the software you are using is suitable for your needs. The problem you have is likely to be not reading the documentation carefully. Note that the default setting of splicedAlignment is FALSE. The default settings are intended to be used with DNA sequencing data, but you have RNA sequencing data. splicedAlignment needs to be TRUE for your case. Many of the reads which would map across splice junctions are probably being discarded by your analysis. You should also provide the R command you used when you ask a question.