I had run DeNovo Assembly on my data using Trinity. The Assembled .fasta file was then aligned by using TopHat without giving an annotation file. The amount of unmapped.bam is more than expected as it ranges anywhere from 100 MB to 600 MB for different conditions. I have 6 different conditions and I have paired-end data.
My question is it normal to get such high number of unmapped reads?
One of the
Left reads: Input : 12382431 Mapped : 11331326 (91.5% of input) of these: 10276265 (90.7%) have multiple alignments (312919 have >20) Right reads: Input : 12382431 Mapped : 11346906 (91.6% of input) of these: 10290863 (90.7%) have multiple alignments (312928 have >20) 91.6% overall read mapping rate. Aligned pairs: 11146003 of these: 10125490 (90.8%) have multiple alignments 65963 ( 0.6%) are discordant alignments 89.5% concordant pair alignment rate.
Should I be concerned?