I have aligned our RNA-seq to reference transcriptome (there is no genome) using bwa mem. The reference transcriptome is from the same species but from different population, so some mismatches and indels are expected.
Then I used eXpress to count reads.
The results are strangely low. No reference contig has more than 60 tot_counts. However, when I look at the alignment in tablet or IGV some contigs have up to 500000 reads aligned to them. Moreover, uniq_counts is equal to tot_counts for all contigs. But cca 0.1% of reads in my bam file are multimapped.
Any suggestions what could be wrong?